Alignments for a candidate for carA in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Sulfurihydrogenibium subterraneum DSM 15120

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_028950746.1 Q385_RS0105715 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000619805.1:WP_028950746.1
          Length = 375

 Score =  369 bits (946), Expect = e-106
 Identities = 182/379 (48%), Positives = 251/379 (66%), Gaps = 5/379 (1%)

Query: 2   IKSALLVLEDGTQFHGRAIGATGSAVG-EVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           ++ A+L LEDG  F+G A  +     G EV+FNTSMTGYQEILTDPSY  QIV +T   +
Sbjct: 1   MEKAILALEDGHFFYGWAFSSPVKETGGEVIFNTSMTGYQEILTDPSYKGQIVVMTAAEV 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GN G N  D++S +V   G V++D+P + SN+R  + L  YL+++N++ I  +DTR + R
Sbjct: 61  GNYGINTEDDQSDRVWVNGFVVKDVPNLYSNYRAVQSLKEYLEKNNVLGIFGVDTRSIVR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LR KG   G I  GD   A  A+ KAR+ P ++ ++L  EV+  + Y WTQ SW    G
Sbjct: 121 ILRTKGVMKGYIGVGDISPAE-AVRKARSIPDISELNLVAEVSKPQVYRWTQKSWRWPNG 179

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
             E   + E  + V   D+G KR+ILR+L DR   L   P   SAE+VL +NPDGIFLSN
Sbjct: 180 YEE---QTEFHYKVAVLDYGVKRDILRLLADRNLELICFPYNASAEEVLSINPDGIFLSN 236

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDPA   Y I  I+K + ++ P+FGICLGHQLL+ A G++T K++FGHHGGNHPVK++
Sbjct: 237 GPGDPAVLTYQIQQIKKLIASEKPIFGICLGHQLLSWAFGSRTYKLEFGHHGGNHPVKNL 296

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           +   V ITAQNH +A DE+ LP ++ +TH +L D T++G+   + P FS Q HPEA+PGP
Sbjct: 297 KTGRVEITAQNHNYATDESKLPGDVEITHINLNDHTVEGMRHKNYPVFSIQHHPEAAPGP 356

Query: 361 HDAAPLFDHFIELIEQYRK 379
           HD+  +FD F  LI++ +K
Sbjct: 357 HDSFYIFDEFYNLIKECKK 375


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: 411
Number of extensions: 12
Number of successful extensions: 4
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: 375
Length adjustment: 30
Effective length of query: 352
Effective length of database: 345
Effective search space:   121440
Effective search space used:   121440
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_028950746.1 Q385_RS0105715 (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.4027737.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-153  494.7   0.0   8.5e-153  494.5   0.0    1.0  1  NCBI__GCF_000619805.1:WP_028950746.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000619805.1:WP_028950746.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.5   0.0  8.5e-153  8.5e-153       1     360 [.       4     371 ..       4     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 494.5 bits;  conditional E-value: 8.5e-153
                             TIGR01368   1 atlvledGtvfegksfgae.kevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkik 72 
                                           a+l+ledG++f g++f+++ ke+ Gev+FnTsmtGYqEiltDpsYkgqivv+t+ ++gnyg+n+ed +s++++
  NCBI__GCF_000619805.1:WP_028950746.1   4 AILALEDGHFFYGWAFSSPvKETGGEVIFNTSMTGYQEILTDPSYKGQIVVMTAAEVGNYGINTEDDQSDRVW 76 
                                           689**************87266779************************************************ PP

                             TIGR01368  73 vkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakes 145
                                           v+g+vvk++ + +snyra +sL+e+l+++++ +i gvDTR++v+ lR+kg+mk++i   +++  e+v+ka++ 
  NCBI__GCF_000619805.1:WP_028950746.1  77 VNGFVVKDVPNLYSNYRAVQSLKEYLEKNNVLGIFGVDTRSIVRILRTKGVMKGYIGVGDISPAEAVRKARSI 149
                                           ************************************************************************* PP

                             TIGR01368 146 pkvkevnlvkevstkeayeleqk........akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsae 210
                                           p+++e+nlv+evs  ++y+++qk        +++++ +++v+v+d+GvK++ilr L++r++e++ +p+++sae
  NCBI__GCF_000619805.1:WP_028950746.1 150 PDISELNLVAEVSKPQVYRWTQKswrwpngyEEQTEFHYKVAVLDYGVKRDILRLLADRNLELICFPYNASAE 222
                                           *********************955666667455666669********************************** PP

                             TIGR01368 211 eikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkd 283
                                           e+ ++npdgi+lsnGPGdPa ++++i+++kkl+ +++PifGIclGhqll+ a+g++tykl+fGh+G+Nhpvk+
  NCBI__GCF_000619805.1:WP_028950746.1 223 EVLSINPDGIFLSNGPGDPAVLTYQIQQIKKLIASEKPIFGICLGHQLLSWAFGSRTYKLEFGHHGGNHPVKN 295
                                           ************************************************************************* PP

                             TIGR01368 284 lktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefv 356
                                           lktgrveit+qNH+ya de+ l+ +++e+th nlnD+tveg++hk++pvfs+Q+HPea+pGphd+ y+Fdef 
  NCBI__GCF_000619805.1:WP_028950746.1 296 LKTGRVEITAQNHNYATDESKLP-GDVEITHINLNDHTVEGMRHKNYPVFSIQHHPEAAPGPHDSFYIFDEFY 367
                                           *******************9976.77*********************************************** PP

                             TIGR01368 357 elik 360
                                           +lik
  NCBI__GCF_000619805.1:WP_028950746.1 368 NLIK 371
                                           *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (375 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: 20.98
//
[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