Alignments for a candidate for carA in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Bacteroides thetaiotaomicron VPI-5482

Align Carbamoyl-phosphate synthase arginine-specific small chain; CPS-A; Arginine-specific carbamoyl-phosphate synthetase, glutamine chain; EC 6.3.5.5 (characterized)
to candidate 350084 BT0556 carbamoyl phosphate synthetase III (glutamine-hydrolyzing) (NCBI ptt file)

Query= SwissProt::P07258
         (411 letters)



>FitnessBrowser__Btheta:350084
          Length = 388

 Score =  343 bits (879), Expect = 7e-99
 Identities = 182/388 (46%), Positives = 236/388 (60%), Gaps = 39/388 (10%)

Query: 9   TFCIQNGPSFEGISFGANKSVAGETVFTTSLVGYPESMTDPSYRGQILVFTQPLIGNYGV 68
           T  + +G  F G SFG  K VAGE VF T++ GYPES+TDPSY GQ++  T PL+GNYGV
Sbjct: 5   TLILDDGSRFSGKSFGYEKPVAGEVVFNTAMTGYPESLTDPSYAGQLMTLTYPLVGNYGV 64

Query: 69  PSGEARDEYNLLKYFESPHIHVVGIVVAEYAYQYSHWTAVESLAQWCQREGVAAITGVDT 128
           P     +   L  + ES  IH   I+V++Y+ +YSHW AVESL  W +RE V  ITG+DT
Sbjct: 65  PPFTI-EPNGLATFMESEKIHAEAIIVSDYSSEYSHWNAVESLGDWLKREKVPGITGIDT 123

Query: 129 RELVQYLREQGSSLGRITL-------ADHDPVPYVNPMKTNLVAQVTTKKPFHVSALP-- 179
           REL + LRE G  +GRI          D+  +   N    N V +V+ K+   +S LP  
Sbjct: 124 RELTKILREHGVMMGRIVFDDEIVGEIDNGQLTMDNYAAVNYVDRVSCKE--IISYLPDG 181

Query: 180 ---------------------GKAKANVALIDCGVKENIIRCLVKRGANVTVFPYDYRIQ 218
                                      V L+DCGVK NIIRCL++RG  V   P+DY   
Sbjct: 182 TSQCFPLSTSIAQLNSQLLTFNSQLKKVVLVDCGVKTNIIRCLLRRGVEVIRVPWDYDFN 241

Query: 219 DVASEFDGIFLSNGPGNPELCQATISNVRELLNNPVYDCIPIFGICLGHQLLALASGAST 278
            +  EFDG+F+SNGPG+P+ C A + N+R+ + N   + +PIFGIC+G+QLL+ A GA  
Sbjct: 242 GL--EFDGLFISNGPGDPDTCDAAVQNIRKAMAN---EKLPIFGICMGNQLLSKAGGAKI 296

Query: 279 HKLKYGNRAHNIPAMDLTTGQCHITSQNHGYAVDPETLPKDQWKPYFVNLNDKSNEGMIH 338
           +KLKYG+R+HN P   + T +C ITSQNHGYAVD  TL  D W+P F+N+ND SNEG+ H
Sbjct: 297 YKLKYGHRSHNQPVRMVGTERCFITSQNHGYAVDNNTLGAD-WEPLFINMNDGSNEGIKH 355

Query: 339 LQRPIFSTQFHPEAKGGPLDTAILFDKF 366
            + P FS QFHPEA  GP DT  LFD+F
Sbjct: 356 KKNPWFSAQFHPEAASGPTDTEFLFDEF 383


Lambda     K      H
   0.318    0.134    0.402 

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: 458
Number of extensions: 20
Number of successful extensions: 6
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: 411
Length of database: 388
Length adjustment: 31
Effective length of query: 380
Effective length of database: 357
Effective search space:   135660
Effective search space used:   135660
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 350084 BT0556 (carbamoyl phosphate synthetase III (glutamine-hydrolyzing) (NCBI ptt file))
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.7648.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   5.2e-139  449.1   0.0   5.9e-139  449.0   0.0    1.0  1  lcl|FitnessBrowser__Btheta:350084  BT0556 carbamoyl phosphate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350084  BT0556 carbamoyl phosphate synthetase III (glutamine-hydrolyzing) (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.0   0.0  5.9e-139  5.9e-139       2     359 ..       5     387 ..       4     388 .] 0.92

  Alignments for each domain:
  == domain 1  score: 449.0 bits;  conditional E-value: 5.9e-139
                          TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneeda.........es 68 
                                        tl+l+dG+ f+gksfg+ek v+GevvFnT+mtGY+E+ltDpsY+gq+++ltypl+gnygv++ ++         es
  lcl|FitnessBrowser__Btheta:350084   5 TLILDDGSRFSGKSFGYEKPVAGEVVFNTAMTGYPESLTDPSYAGQLMTLTYPLVGNYGVPPFTIepnglatfmES 80 
                                        79************************************************************999999******** PP

                          TIGR01368  69 kkikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekake 144
                                        +ki++++++v+++s+e+s+++a esL ++lk+e++++i+g+DTR+l+k lRe+g+m+++i+ +++   e  +   +
  lcl|FitnessBrowser__Btheta:350084  81 EKIHAEAIIVSDYSSEYSHWNAVESLGDWLKREKVPGITGIDTRELTKILREHGVMMGRIVFDDEIVGEIDNGQLT 156
                                        *************************************************************999776555555555 PP

                          TIGR01368 145 spkvkevnlvkevstkeayeleq..............k.....akkegkklrvvvidlGvKenilreLvkrgvevt 201
                                          + + vn+v++vs+ke +++                +      + +++ ++vv++d+GvK+ni+r+L++rgvev+
  lcl|FitnessBrowser__Btheta:350084 157 MDNYAAVNYVDRVSCKEIISYLPdgtsqcfplstsiaQlnsqlLTFNSQLKKVVLVDCGVKTNIIRCLLRRGVEVI 232
                                        6666679************999878887777776665155555344444478************************ PP

                          TIGR01368 202 vvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkkllea.kiPifGIclGhqllalalgaktyklkfGhrG 276
                                         vp+d++++    l+ dg+++snGPGdP+++++a+++++k++ + k+PifGIc+G+qll++a gak+yklk+Ghr 
  lcl|FitnessBrowser__Btheta:350084 233 RVPWDYDFN---GLEFDGLFISNGPGDPDTCDAAVQNIRKAMANeKLPIFGICMGNQLLSKAGGAKIYKLKYGHRS 305
                                        *******99...67779**********************9887669****************************** PP

                          TIGR01368 277 aNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylF 352
                                        +N+pv+ + t+r++itsqNHgyavd+++l   ++e+ + n+nDg++eg++hk+ p fs Q+HPea++Gp+dte+lF
  lcl|FitnessBrowser__Btheta:350084 306 HNQPVRMVGTERCFITSQNHGYAVDNNTLG-ADWEPLFINMNDGSNEGIKHKKNPWFSAQFHPEAASGPTDTEFLF 380
                                        ***************************976.66******************************************* PP

                          TIGR01368 353 defveli 359
                                        defv+l+
  lcl|FitnessBrowser__Btheta:350084 381 DEFVNLL 387
                                        ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (388 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.47
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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 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 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