Alignments for a candidate for carA in Paucidesulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Paucidesulfovibrio gracilis DSM 16080

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_078716276.1 B5D49_RS03560 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_900167125.1:WP_078716276.1
          Length = 373

 Score =  323 bits (829), Expect = 3e-93
 Identities = 167/368 (45%), Positives = 227/368 (61%), Gaps = 19/368 (5%)

Query: 1   MKRRLVLENGAVFEGEAF-GSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIG 59
           MK  L LE+G +F GE+F G ++ N GEV+FNTGMTGYQE+L+DPSY GQ+V +TYPLIG
Sbjct: 1   MKAILALEDGTLFPGESFTGPIKAN-GEVIFNTGMTGYQEVLTDPSYAGQMVCMTYPLIG 59

Query: 60  NYGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRM 119
           NYG+N +D ES    V G I+KE C+LPSNWRS   L EYL    + G++G+DTR LTR 
Sbjct: 60  NYGVNPEDVESDRIQVAGFIVKECCKLPSNWRSTRPLPEYLAEAGVAGIEGVDTRALTRH 119

Query: 120 IRTAGALKGTFASSDEDIEAVLKRLNETELPRNQ--VSQVSAKTAY-------------- 163
           +R  GA++G  ++  +D  A++++     L + Q    +VS    Y              
Sbjct: 120 LRLHGAMRGVISTQVDDTAALVEQARNIPLMQGQNLADRVSTDQPYLWTENGPETVNLND 179

Query: 164 -PSPGRGKRIVLVDFGMKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGD 222
              P  G R+V+ DFG+K  I R L  +    + VP    A++V  LKPD + LSNGPGD
Sbjct: 180 FQWPDGGPRLVVYDFGIKWNIHRLLADQGFVQLTVPSGFAADDVRALKPDAVFLSNGPGD 239

Query: 223 PKDVPEAIEMIKGVLGKVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKV 282
           P  V  A+E  + +    P+ GICLGHQ+  LA G  T K+ FGH G NHPV +L T K+
Sbjct: 240 PAVVTGAVEATRDLCEDTPVGGICLGHQILGLALGGTTFKLPFGHHGCNHPVMDLETEKI 299

Query: 283 ALTSQNHGYTVSSISKTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHL 342
            ++SQNHG+ V       L++TH  +NDDT+EG  H+  P   +Q+HPEA+PGP D+ + 
Sbjct: 300 EISSQNHGFCVDISGLNHLKMTHRNLNDDTLEGFAHRDKPVIAIQFHPEAAPGPHDSGYF 359

Query: 343 FDRFIEMI 350
           F RF EM+
Sbjct: 360 FARFREMV 367


Lambda     K      H
   0.317    0.136    0.397 

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: 402
Number of extensions: 12
Number of successful extensions: 2
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: 364
Length of database: 373
Length adjustment: 30
Effective length of query: 334
Effective length of database: 343
Effective search space:   114562
Effective search space used:   114562
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_078716276.1 B5D49_RS03560 (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.1046700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-141  455.4   0.0   7.4e-141  455.2   0.0    1.0  1  NCBI__GCF_900167125.1:WP_078716276.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167125.1:WP_078716276.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.2   0.0  7.4e-141  7.4e-141       1     360 [.       3     368 ..       3     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 455.2 bits;  conditional E-value: 7.4e-141
                             TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikv 73 
                                           a+l+ledGt f g+sf  + ++ Gev+FnT+mtGYqE+ltDpsY+gq+v +typlignygvn+ed+es++i+v
  NCBI__GCF_900167125.1:WP_078716276.1   3 AILALEDGTLFPGESFTGPIKANGEVIFNTGMTGYQEVLTDPSYAGQMVCMTYPLIGNYGVNPEDVESDRIQV 75 
                                           689********************************************************************** PP

                             TIGR01368  74 kglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakesp 146
                                           +g++vke++k +sn+r+++ L e+l+e g+++iegvDTRal+++lR +g+m++vist+  ++  lve+a++ p
  NCBI__GCF_900167125.1:WP_078716276.1  76 AGFIVKECCKLPSNWRSTRPLPEYLAEAGVAGIEGVDTRALTRHLRLHGAMRGVISTQVDDTAALVEQARNIP 148
                                           ************************************************************************* PP

                             TIGR01368 147 kvkevnlvkevstkeayeleq......k...akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsae 210
                                            ++++nl+++vst+++y +++      +    +  +   r+vv+d+G+K ni r L+++g+    vp  + a+
  NCBI__GCF_900167125.1:WP_078716276.1 149 LMQGQNLADRVSTDQPYLWTEngpetvNlndFQWPDGGPRLVVYDFGIKWNIHRLLADQGFVQLTVPSGFAAD 221
                                           ********************96666551555444444459********************************* PP

                             TIGR01368 211 eikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkd 283
                                           ++ +l+pd+++lsnGPGdPa v+ a+e ++ l+e ++P+ GIclGhq+l+lalg+ t+kl fGh+G Nhpv+d
  NCBI__GCF_900167125.1:WP_078716276.1 222 DVRALKPDAVFLSNGPGDPAVVTGAVEATRDLCE-DTPVGGICLGHQILGLALGGTTFKLPFGHHGCNHPVMD 293
                                           **********************************.************************************** PP

                             TIGR01368 284 lktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefv 356
                                           l+t+++ei+sqNHg+ vd + l+  +l++th+nlnD+t+eg +h+++pv+++Q+HPea+pGphd+ y+F +f 
  NCBI__GCF_900167125.1:WP_078716276.1 294 LETEKIEISSQNHGFCVDISGLN--HLKMTHRNLNDDTLEGFAHRDKPVIAIQFHPEAAPGPHDSGYFFARFR 364
                                           *******************9865..79*********************************************9 PP

                             TIGR01368 357 elik 360
                                           e+++
  NCBI__GCF_900167125.1:WP_078716276.1 365 EMVR 368
                                           9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (373 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.43
//
[ok]

This GapMind analysis is from Jul 25 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 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