GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Phyllobacterium brassicacearum STM 196

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_106710507.1 CU102_RS07170 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_003010955.1:WP_106710507.1
          Length = 407

 Score =  353 bits (905), Expect = e-102
 Identities = 190/382 (49%), Positives = 246/382 (64%), Gaps = 14/382 (3%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           +A+LVL DGT   G+ +GATG    EV FNT++TGY+EILTDPSY+ QIVT T+PHIGNV
Sbjct: 17  TAVLVLADGTVIEGKGLGATGICEAEVCFNTALTGYEEILTDPSYAGQIVTFTFPHIGNV 76

Query: 64  GTNDADEE----SSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119
           GTN  D E    +++  A G + +      S++R  E L  +LK   ++A+A  DTR LT
Sbjct: 77  GTNKEDIEDLTPANRAGAVGAIFKADITAPSSYRAAEHLDHWLKARGVIALAGADTRALT 136

Query: 120 RLLREKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSW 175
            L+REKG  N  +IA D PD    +     +A A+ GL  +DLAK+VT+ ++  WT+  W
Sbjct: 137 VLIREKGMPNA-VIAHD-PDGKFDIPALKARAAAWHGLLDLDLAKDVTSGQSSVWTEKPW 194

Query: 176 TLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDG 235
               G  +   + +  FHVVA D+G KRNILR++   G ++TI+PA  +A DVL   PDG
Sbjct: 195 VWNEGFDD---QSDPEFHVVAIDYGIKRNILRLIAGLGAKVTILPASATAADVLAYKPDG 251

Query: 236 IFLSNGPGDPAPCD-YAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGN 294
           IFLSNGPGDPA    YA+ AI++ ++TDIPVFGICLGHQ+LALA G  T KM  GHHG N
Sbjct: 252 IFLSNGPGDPAATGKYAVPAIKELIKTDIPVFGICLGHQMLALALGGDTKKMHQGHHGAN 311

Query: 295 HPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHP 354
           HPV+D     V I + NHGFAVD  + P  +  TH SLFDG+  G+    +P FS Q HP
Sbjct: 312 HPVRDDTTGKVEIVSMNHGFAVDAGSFPDGVEETHVSLFDGSNCGLRVVGRPVFSVQHHP 371

Query: 355 EASPGPHDAAPLFDHFIELIEQ 376
           EASPGP D+  LF  F  LI +
Sbjct: 372 EASPGPQDSHYLFRRFFNLIRE 393


Lambda     K      H
   0.318    0.135    0.400 

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: 479
Number of extensions: 21
Number of successful extensions: 5
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: 382
Length of database: 407
Length adjustment: 31
Effective length of query: 351
Effective length of database: 376
Effective search space:   131976
Effective search space used:   131976
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: 50 (23.9 bits)

Align candidate WP_106710507.1 CU102_RS07170 (glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small 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/TIGR01368.hmm
# target sequence database:        /tmp/gapView.3348140.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01368  [M=361]
Accession:   TIGR01368
Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-124  400.1   0.0   4.8e-124  399.9   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106710507.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106710507.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.9   0.0  4.8e-124  4.8e-124       1     360 [.      18     392 ..      18     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 399.9 bits;  conditional E-value: 4.8e-124
                             TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneeda....esk 69 
                                           a+lvl+dGtv+egk++ga++ + +ev+FnT++tGY+EiltDpsY+gqiv++t p+ign+g+n+ed+     ++
  NCBI__GCF_003010955.1:WP_106710507.1  18 AVLVLADGTVIEGKGLGATGICEAEVCFNTALTGYEEILTDPSYAGQIVTFTFPHIGNVGTNKEDIedltPAN 90 
                                           689***************************************************************3333367 PP

                             TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelv 139
                                           +  + g + k   +++s+yra e L+++lk +g++a++g DTRal+  +Rekg  +avi+++         l+
  NCBI__GCF_003010955.1:WP_106710507.1  91 RAGAVGAIFKADITAPSSYRAAEHLDHWLKARGVIALAGADTRALTVLIREKGMPNAVIAHDPDGkfdIPALK 163
                                           88999*******************************************************9986544355677 PP

                             TIGR01368 140 ekakespkvkevnlvkevstkeayeleqk........akkegkklrvvvidlGvKenilreLvkrgvevtvvp 204
                                           ++a++ + + +++l+k+v+  + + +++k          +++ + +vv+id+G+K+nilr ++  g++vt++p
  NCBI__GCF_003010955.1:WP_106710507.1 164 ARAAAWHGLLDLDLAKDVTSGQSSVWTEKpwvwnegfDDQSDPEFHVVAIDYGIKRNILRLIAGLGAKVTILP 236
                                           77778888999*************999955556667677788889**************************** PP

                             TIGR01368 205 adtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrG 276
                                           a+++a+++ +++pdgi+lsnGPGdPaa  ++a+  +k+l++++iP+fGIclGhq+lalalg++t k++ Gh+G
  NCBI__GCF_003010955.1:WP_106710507.1 237 ASATAADVLAYKPDGIFLSNGPGDPAATgKYAVPAIKELIKTDIPVFGICLGHQMLALALGGDTKKMHQGHHG 309
                                           *************************776377899*************************************** PP

                             TIGR01368 277 aNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdte 349
                                           aNhpv+d +tg+vei s NHg+avd  s + + +e thv+l+Dg++ gl+    pvfsvQ+HPeaspGp+d++
  NCBI__GCF_003010955.1:WP_106710507.1 310 ANHPVRDDTTGKVEIVSMNHGFAVDAGSFP-DGVEETHVSLFDGSNCGLRVVGRPVFSVQHHPEASPGPQDSH 381
                                           ****************************77.55**************************************** PP

                             TIGR01368 350 ylFdefvelik 360
                                           ylF++f++li+
  NCBI__GCF_003010955.1:WP_106710507.1 382 YLFRRFFNLIR 392
                                           ********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (407 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.30
//
[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:

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:

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:

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:

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