Alignments for a candidate for carB in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Phyllobacterium endophyticum PEPV15

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_106718691.1 CU100_RS20965 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_003010935.1:WP_106718691.1
          Length = 1161

 Score = 1270 bits (3287), Expect = 0.0
 Identities = 684/1146 (59%), Positives = 813/1146 (70%), Gaps = 91/1146 (7%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILI+GAGPI+IGQACEFDYSG QACKAL+EEGYRVILVNSNPATIMTDPE+
Sbjct: 1    MPKRTDIKSILIIGAGPIIIGQACEFDYSGTQACKALKEEGYRVILVNSNPATIMTDPEL 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI  EVV KII KERPDA+LPTMGGQTALN AL L R GVL+ + V MIGA A
Sbjct: 61   ADATYIEPITPEVVAKIIAKERPDALLPTMGGQTALNTALSLRRMGVLDRYNVEMIGANA 120

Query: 121  DAIDKAEDRRRF----------------------------------------------DV 134
            +AIDKAEDR  F                                              D 
Sbjct: 121  EAIDKAEDRALFREAMAKIGLETPKSMLANATEVKDLDRKLHQEQREAVKAKYSGPELDA 180

Query: 135  AMKKIGLE-------TARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREE 187
            A+ K+  E         +  ++H +  A A    VG P IIRPSFTMGG+GGGIAYNR E
Sbjct: 181  ALDKLETEWQLGEGDRKQRYVSHALGMAGAALDHVGLPAIIRPSFTMGGTGGGIAYNRSE 240

Query: 188  FEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDS 247
            F EI   GLD SPT E+LI+ES++GWKEYEMEVVRDK DNCII+CSIEN D MG+HTGDS
Sbjct: 241  FYEIIGSGLDASPTTEVLIEESVLGWKEYEMEVVRDKADNCIIICSIENVDPMGVHTGDS 300

Query: 248  ITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSRS 307
            ITVAPA TLTDKEYQIMRNAS+AVLREIGVETGGSNVQFAVNP+NGRLIVIEMNPRVSRS
Sbjct: 301  ITVAPALTLTDKEYQIMRNASIAVLREIGVETGGSNVQFAVNPENGRLIVIEMNPRVSRS 360

Query: 308  SALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPRFNFEKF 367
            SALASKATGFPIAK+AAKLAVGYTLDEL NDITGG TPASFEPSIDYVVTKIPRF FEKF
Sbjct: 361  SALASKATGFPIAKIAAKLAVGYTLDELDNDITGGATPASFEPSIDYVVTKIPRFAFEKF 420

Query: 368  AGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV--SLDDPEALTKIR 425
             GA   LTT MKSVGEVMAIGRT +ESLQKALRGLE G TG D      L +      IR
Sbjct: 421  PGAEPTLTTAMKSVGEVMAIGRTFKESLQKALRGLETGLTGLDEIAIPGLGEGNDNNAIR 480

Query: 426  RELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLN 485
              +     DR+  +  A R GLSV+ V     ID WFL Q+ E++  EE+V E G+   +
Sbjct: 481  AAIGVPTPDRLRMVGQALRLGLSVEEVHEGCKIDPWFLEQMAEIIATEERVREHGLP-KD 539

Query: 486  ADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYS 545
            A  LR LK  GF+DARLA LA V   E+ KLR + ++HPV+KR+DTCAAEFA+ TAYMYS
Sbjct: 540  AQNLRMLKGMGFSDARLASLARVDPGEVTKLRHRLEVHPVFKRIDTCAAEFASPTAYMYS 599

Query: 546  TYEEECEANPS-----TDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            TYE     +P+     +DR+K+++LGGGPNRIGQGIEFDYCC HA+ ALR+ GYE IM+N
Sbjct: 600  TYETPFAGSPASEAQVSDRKKVVILGGGPNRIGQGIEFDYCCCHAAFALRDAGYEAIMIN 659

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKP----KGVIVQYGGQTPLKLARALEA 656
            CNPETVSTDYDTSDRLYFEP+T EDVLEI+R+E+      GVIVQ+GGQTPLKLA ALE 
Sbjct: 660  CNPETVSTDYDTSDRLYFEPLTAEDVLEILRVEQTAGTLHGVIVQFGGQTPLKLADALEK 719

Query: 657  AGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRP 716
            AG+P++GTSPDAID AEDR+RFQ  + +L L QP N    ++E A   A E+G+PLVVRP
Sbjct: 720  AGIPILGTSPDAIDLAEDRDRFQKLLIKLDLTQPKNGIAYSVEQARTIAGELGFPLVVRP 779

Query: 717  SYVLGGRAMEIVYDEADLRRYFQTAV----------SVSNDA-----------PVLLDHF 755
            SYVLGGRAM+I++DE  L+ Y    V             ND            P+L D +
Sbjct: 780  SYVLGGRAMQIIHDERGLQSYLLDTVPELVPEDIKQKYPNDKTGQINTLLGKNPLLFDRY 839

Query: 756  LDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQK 815
            L +A+EVDVD +CDG+   I GIMEHIE+AG+HSGDSACSLP ++LS E    + ++   
Sbjct: 840  LSEAIEVDVDCLCDGKDTWISGIMEHIEEAGIHSGDSACSLPVHSLSTETVAELEKETAA 899

Query: 816  LAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLA 875
            LA  L V GLMNVQ+A+K+  +Y++EVNPRA+RTVPFV+K  G P+AKVAAR+MAG++L 
Sbjct: 900  LAKSLNVVGLMNVQYAIKDGTIYVLEVNPRASRTVPFVAKTIGTPIAKVAARIMAGETLE 959

Query: 876  EQ-----GVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAK 930
            E      G        + +VKE V PF +FPGVD LLGPEMRSTGEVMG+   +A AFAK
Sbjct: 960  EALAHYGGKPSNTGRKHIAVKEAVFPFARFPGVDTLLGPEMRSTGEVMGLDYDYALAFAK 1019

Query: 931  AQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRL 990
            +QLG+   + + G   +SVR+ DK+R++    +L   GF++ AT GTA  LGE G+  + 
Sbjct: 1020 SQLGAGVDLPRDGTLFVSVRDEDKQRILAPVKRLAALGFKILATGGTARFLGENGVEAQK 1079

Query: 991  VNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFAT 1050
            +NKV EGRPH++D I+N +   + NTT   +AI DS+ +RR+ L  KV Y TTL+G  A 
Sbjct: 1080 INKVQEGRPHVEDAIRNRQVQLVFNTTDSAKAISDSKSLRRATLMQKVPYYTTLSGADAV 1139

Query: 1051 AMALNA 1056
            A A+ A
Sbjct: 1140 AEAIAA 1145


Lambda     K      H
   0.318    0.135    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3320
Number of extensions: 164
Number of successful extensions: 20
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 1073
Length of database: 1161
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1115
Effective search space:  1145105
Effective search space used:  1145105
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

Align candidate WP_106718691.1 CU100_RS20965 (carbamoyl-phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01369.hmm
# target sequence database:        /tmp/gapView.1809063.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01369  [M=1052]
Accession:   TIGR01369
Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1460.6   0.0          0 1205.2   0.0    2.5  2  NCBI__GCF_003010935.1:WP_106718691.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106718691.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.3   0.1   3.8e-79   3.8e-79       1     152 [.       2     153 ..       2     162 .. 0.97
   2 ! 1205.2   0.0         0         0     146    1051 ..     200    1142 ..     190    1143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 252.3 bits;  conditional E-value: 3.8e-79
                             TIGR01369   1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveav 73 
                                           pkr+dik++l+iG+Gpi+igqA+EFDYsG+qa+kalkeeg++v+Lvnsn+At+mtd+elad++YieP+t+e+v
  NCBI__GCF_003010935.1:WP_106718691.1   2 PKRTDIKSILIIGAGPIIIGQACEFDYSGTQACKALKEEGYRVILVNSNPATIMTDPELADATYIEPITPEVV 74 
                                           689********************************************************************** PP

                             TIGR01369  74 ekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakse 146
                                           +kii kErpDa+l+t+GGqtaLn a++l+++GvL++y+v+++G++ eai+kaedR +F+ea+++i++e++ks 
  NCBI__GCF_003010935.1:WP_106718691.1  75 AKIIAKERPDALLPTMGGQTALNTALSLRRMGVLDRYNVEMIGANAEAIDKAEDRALFREAMAKIGLETPKSM 147
                                           ************************************************************************9 PP

                             TIGR01369 147 ivesve 152
                                            ++ +e
  NCBI__GCF_003010935.1:WP_106718691.1 148 LANATE 153
                                           987654 PP

  == domain 2  score: 1205.2 bits;  conditional E-value: 0
                             TIGR01369  146 eivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiE 216 
                                             + +    a +a +++g+P i+R++ft+gGtG+gia+n++e+ e++ ++l+asp+++vl+e+s+ gwkE+E
  NCBI__GCF_003010935.1:WP_106718691.1  200 YVSHALGMAGAALDHVGLPAIIRPSFTMGGTGGGIAYNRSEFYEIIGSGLDASPTTEVLIEESVLGWKEYE 270 
                                            55566677888999********************************************************* PP

                             TIGR01369  217 yEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfal 286 
                                            +EvvRD++dncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+as++++re+gve++ +nvqfa+
  NCBI__GCF_003010935.1:WP_106718691.1  271 MEVVRDKADNCIIICSIENVDPMGVHTGDSITVAPALTLTDKEYQIMRNASIAVLREIGVETGgSNVQFAV 341 
                                            *************************************************************988******* PP

                             TIGR01369  287 dPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvki 356 
                                            +Pe+ r++viE+npRvsRssALAskAtG+PiAk+aaklavGy+Ldel nd+t+  t+AsfEPs+DYvv+ki
  NCBI__GCF_003010935.1:WP_106718691.1  342 NPENGRLIVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELDNDITGgATPASFEPSIDYVVTKI 412 
                                            ****************************************************878**************** PP

                             TIGR01369  357 PrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg...lklke.keaesdeeleeal 423 
                                            Pr++++kf +++ +l+t mksvGEvmaigrtf+e+lqkalr le++l+g   + ++   e +++++++ a+
  NCBI__GCF_003010935.1:WP_106718691.1  413 PRFAFEKFPGAEPTLTTAMKSVGEVMAIGRTFKESLQKALRGLETGLTGldeIAIPGlGEGNDNNAIRAAI 483 
                                            *************************************************433333331356778889999* PP

                             TIGR01369  424 kkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsd 494 
                                              p+++Rl ++ +alr g+sveev+e +kid +fle++++++++e++++e+ l   ++++l+ +k +Gfsd
  NCBI__GCF_003010935.1:WP_106718691.1  484 GVPTPDRLRMVGQALRLGLSVEEVHEGCKIDPWFLEQMAEIIATEERVREHGLP-KDAQNLRMLKGMGFSD 553 
                                            *************************************************88887.7999************ PP

                             TIGR01369  495 eqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvlvl 560 
                                            +++a+l++v+  ev+klr++l+++pv+kr+Dt+aaEf + t+Y+Ystye+        +++v+++kkv++l
  NCBI__GCF_003010935.1:WP_106718691.1  554 ARLASLARVDPGEVTKLRHRLEVHPVFKRIDTCAAEFASPTAYMYSTYETPfagspASEAQVSDRKKVVIL 624 
                                            *************************************************987777789999********** PP

                             TIGR01369  561 GsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekv. 630 
                                            G+Gp+Rigqg+EFDyc+ ha+ alr+agy++i+in+nPEtvstDyd++drLyFe+lt edvl+i++ e++ 
  NCBI__GCF_003010935.1:WP_106718691.1  625 GGGPNRIGQGIEFDYCCCHAAFALRDAGYEAIMINCNPETVSTDYDTSDRLYFEPLTAEDVLEILRVEQTa 695 
                                            ********************************************************************963 PP

                             TIGR01369  631 ...egvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeake 698 
                                               +gvivq+gGqt+l+la++le+ag++ilGts+++id aEdR++F+kll +l++ qpk+ +a sve+a++
  NCBI__GCF_003010935.1:WP_106718691.1  696 gtlHGVIVQFGGQTPLKLADALEKAGIPILGTSPDAIDLAEDRDRFQKLLIKLDLTQPKNGIAYSVEQART 766 
                                            33368****************************************************************** PP

                             TIGR01369  699 iakeigyPvlvRpsyvlgGrameiveneeeleryle.....................eavevskekPvlid 748 
                                            ia e+g+P++vRpsyvlgGram+i+++e  l++yl                      +++++  ++P+l d
  NCBI__GCF_003010935.1:WP_106718691.1  767 IAGELGFPLVVRPSYVLGGRAMQIIHDERGLQSYLLdtvpelvpedikqkypndktgQINTLLGKNPLLFD 837 
                                            *********************************99767777888888777777665556667789****** PP

                             TIGR01369  749 kyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkG 819 
                                            +yl++a+EvdvD ++dg++  i gi+eHiEeaG+HsGDs+++lp ++ls+e++ ++++ ++++ak+l+v+G
  NCBI__GCF_003010935.1:WP_106718691.1  838 RYLSEAIEVDVDCLCDGKDTWISGIMEHIEEAGIHSGDSACSLPVHSLSTETVAELEKETAALAKSLNVVG 908 
                                            *********************************************************************** PP

                             TIGR01369  820 llniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleele...kgvkkekksklvav 887 
                                            l+n+q+++kd+++yv+Evn+RasRtvPfv+k++g p++k+a+++++g++lee+     g  +++  k++av
  NCBI__GCF_003010935.1:WP_106718691.1  909 LMNVQYAIKDGTIYVLEVNPRASRTVPFVAKTIGTPIAKVAARIMAGETLEEALahyGGKPSNTGRKHIAV 979 
                                            ***************************************************987554456788899***** PP

                             TIGR01369  888 kaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellela 958 
                                            k+avf+f+++ gvd +lgpem+stGEvmg+++d + a++k++l ++  ++++g++++sv+d+dk+++l+ +
  NCBI__GCF_003010935.1:WP_106718691.1  980 KEAVFPFARFPGVDTLLGPEMRSTGEVMGLDYDYALAFAKSQLGAGVDLPRDGTLFVSVRDEDKQRILAPV 1050
                                            *********************************************************************** PP

                             TIGR01369  959 kklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirr 1029
                                            k+la++g+k++at gta++l e+g++a++++kv+e ++++ +++++++++lv+n+t+ ++ka ++++++rr
  NCBI__GCF_003010935.1:WP_106718691.1 1051 KRLAALGFKILATGGTARFLGENGVEAQKINKVQEGRPHVEDAIRNRQVQLVFNTTD-SAKAISDSKSLRR 1120
                                            ******************************************************998.66688899***** PP

                             TIGR01369 1030 eaveykvplvteletaeallea 1051
                                            +++++kvp+ t+l++a a++ea
  NCBI__GCF_003010935.1:WP_106718691.1 1121 ATLMQKVPYYTTLSGADAVAEA 1142
                                            *****************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1161 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 15.20
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis