Alignments for a candidate for acs in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Mesorhizobium ciceri WSM1271

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate YP_004140376.1 Mesci_1162 acetate/CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000185905.1:YP_004140376.1
          Length = 651

 Score =  895 bits (2314), Expect = 0.0
 Identities = 423/648 (65%), Positives = 511/648 (78%), Gaps = 3/648 (0%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
           MS++H H +        LI+   Y   Y  S+  PD FWG+ GK +DW KP+ KVKNTSF
Sbjct: 1   MSEVHVHRVQPAWKKNALIDNDTYLKWYADSVKNPDKFWGKHGKRIDWFKPFSKVKNTSF 60

Query: 61  APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
             G VSIKW+EDG  N++ NC+DRHL++ G++TAIIWEGD+    K ++Y EL+  VCR 
Sbjct: 61  -DGKVSIKWFEDGLTNVSYNCIDRHLKKRGNQTAIIWEGDNPYDDKKVTYNELYEHVCRL 119

Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
           AN + + G+KKGD V IYMPM+PEAA AMLAC RIGAVHS++FGGFSP+A+AGRI D  S
Sbjct: 120 ANVMKKHGVKKGDRVTIYMPMIPEAAYAMLACTRIGAVHSIVFGGFSPDALAGRIDDCKS 179

Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNV--TSVEHVVVLKRTGGKIDWQEGRDLWWH 238
             VIT+DEG+R G+ IPLK+N D A++      T VE VVV++RTGGK  W  GRD+W+H
Sbjct: 180 TFVITADEGLRGGKPIPLKENTDRAIEIAAKAGTKVEKVVVVRRTGGKTGWVSGRDVWYH 239

Query: 239 DLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPG 298
           D +     + + E+M AEDPLFILYTSGSTGKPKGVLHTT GYLVY ++T +YVFDYH G
Sbjct: 240 DEIATVKAECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTAGYLVYVSMTHQYVFDYHDG 299

Query: 299 DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAP 358
           DIYWCTADVGWVTGHSY++YGPLA GATTLMFEGVPN+P+ +R  +V+DKH+VNI YTAP
Sbjct: 300 DIYWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPSQSRFWEVIDKHKVNIFYTAP 359

Query: 359 TAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTET 418
           TA+RALM  GD  ++ T R SLR+LGSVGEPINPEAWEWY+  +GN K P+VDTWWQTET
Sbjct: 360 TALRALMGAGDAHVKKTSRKSLRVLGSVGEPINPEAWEWYFNVVGNGKVPIVDTWWQTET 419

Query: 419 GGFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLF 478
           GG +ITPLPGAT+LKAGSATRPFFG++P LVD EG  LEGA +G+L ITDSWPGQ RT++
Sbjct: 420 GGILITPLPGATDLKAGSATRPFFGIKPQLVDGEGKVLEGAADGNLCITDSWPGQMRTVY 479

Query: 479 GDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA 538
           GDH+RF QTYFST+K  YF+GDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALV+
Sbjct: 480 GDHDRFVQTYFSTYKGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVS 539

Query: 539 HPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHW 598
           H K++EAAVVG PH+IKGQ IY+YVTL  G EP+ EL  E+   VRKEIG +A+PD + +
Sbjct: 540 HEKVSEAAVVGYPHDIKGQGIYSYVTLMKGAEPTEELRKELVAHVRKEIGAIASPDKIQF 599

Query: 599 TDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
              LPKTRSGKIMRRILRKIA  D S LGDTSTLADP VV+ L+  +Q
Sbjct: 600 APGLPKTRSGKIMRRILRKIAEDDFSALGDTSTLADPAVVDDLVANRQ 647


Lambda     K      H
   0.317    0.135    0.421 

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: 1474
Number of extensions: 61
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 652
Length of database: 651
Length adjustment: 38
Effective length of query: 614
Effective length of database: 613
Effective search space:   376382
Effective search space used:   376382
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: 54 (25.4 bits)

Align candidate YP_004140376.1 Mesci_1162 (acetate/CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# 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.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.3723678.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
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 1048.5   1.0          0 1048.3   1.0    1.0  1  NCBI__GCF_000185905.1:YP_004140376.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000185905.1:YP_004140376.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1048.3   1.0         0         0       3     627 ..      20     643 ..      18     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1048.3 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++++y ++y++++++p+kfw+k++k +++w+kpf+kv+++s++   ++kWfedg +nvsync+drh++kr ++
  NCBI__GCF_000185905.1:YP_004140376.1  20 DNDTYLKWYADSVKNPDKFWGKHGK-RIDWFKPFSKVKNTSFDGkvSIKWFEDGLTNVSYNCIDRHLKKRGNQ 91 
                                           6789*********************.5**************9987799************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwegd++  d +k+tY+el+++vcrlanv+k++Gvkkgdrv+iY+pmipea++amlac+RiGavhs+vf+
  NCBI__GCF_000185905.1:YP_004140376.1  92 TAIIWEGDNPY-DDKKVTYNELYEHVCRLANVMKKHGVKKGDRVTIYMPMIPEAAYAMLACTRIGAVHSIVFG 163
                                           ********998.59*********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216
                                           Gfs++ala Ri d+++ +vitadeglRggk i+lk+++d+a+e a +   +vekv+vv+rtg + + w++grD
  NCBI__GCF_000185905.1:YP_004140376.1 164 GFSPDALAGRIDDCKSTFVITADEGLRGGKPIPLKENTDRAIEIAAKagtKVEKVVVVRRTGGK-TGWVSGRD 235
                                           ******************************************987666779*************.56****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           vw+++++++ ++aec+pek+++edplfiLYtsGstGkPkGvlhtt+Gyl+++++t++yvfd++d+di+wCtaD
  NCBI__GCF_000185905.1:YP_004140376.1 236 VWYHDEIAT-VKAECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTAGYLVYVSMTHQYVFDYHDGDIYWCTAD 307
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGWvtGhsYivygPLanGattl+fegvp+yp++srfwevi+k+kv+ifYtaPta+Ralm +g+++vkk++++s
  NCBI__GCF_000185905.1:YP_004140376.1 308 VGWVTGHSYIVYGPLANGATTLMFEGVPNYPSQSRFWEVIDKHKVNIFYTAPTALRALMGAGDAHVKKTSRKS 380
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lrvlgsvGepinpeaweWy++vvG++k+pivdtwWqtetGgilitplpg at+lk+gsat+P+fGi++++vd 
  NCBI__GCF_000185905.1:YP_004140376.1 381 LRVLGSVGEPINPEAWEWYFNVVGNGKVPIVDTWWQTETGGILITPLPG-ATDLKAGSATRPFFGIKPQLVDG 452
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           egk +e  ++ g L+i+++wP+++rt+ygd++rfv+tYf+++kg yftGDg+rrd+dGy+wi+GRvDdvinvs
  NCBI__GCF_000185905.1:YP_004140376.1 453 EGKVLEGAAD-GNLCITDSWPGQMRTVYGDHDRFVQTYFSTYKGKYFTGDGCRRDADGYYWITGRVDDVINVS 524
                                           *****98777.79************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghr+gtae+esalvshe+v+eaavvg+p++ikg+ i+++v+l++g+e++ee l+kel ++vrkeig+ia+pdk
  NCBI__GCF_000185905.1:YP_004140376.1 525 GHRMGTAEVESALVSHEKVSEAAVVGYPHDIKGQGIYSYVTLMKGAEPTEE-LRKELVAHVRKEIGAIASPDK 596
                                           *************************************************95.********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           i++++ lPktRsGkimRR+lrkiae++ ++lgd+stl+dp+vv++l 
  NCBI__GCF_000185905.1:YP_004140376.1 597 IQFAPGLPKTRSGKIMRRILRKIAEDDfSALGDTSTLADPAVVDDLV 643
                                           *******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (651 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.36
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources