Alignments for a candidate for carA in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_075385892.1 BK574_RS23580 carbamoyl phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_002019605.1:WP_075385892.1
          Length = 359

 Score =  296 bits (759), Expect = 4e-85
 Identities = 166/362 (45%), Positives = 218/362 (60%), Gaps = 13/362 (3%)

Query: 1   MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60
           MK  LVL  G  FEGE  G      GEVVF TGMTGYQE+++DPS+ GQIV  TYPLIGN
Sbjct: 1   MKGYLVLSTGETFEGEWVGQEVDVYGEVVFFTGMTGYQEVITDPSFKGQIVVFTYPLIGN 60

Query: 61  YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120
           YG+N  D ES  P V G+I+ E      ++ S  +  +  +  NIP L GIDTR + + I
Sbjct: 61  YGVNDFDNESKHPQVSGVIMSECNPSGFHYESKQSFQDNCESSNIPMLTGIDTRAVVKRI 120

Query: 121 RTAGALKGTFASSDEDIEAVLKRLNETELPR----NQVSQVSAKTAYPSPGRGKRIVLVD 176
           R  G + G   ++D      L R+N  +       N V +VS K           +VL+D
Sbjct: 121 RELGDM-GAIITTD------LSRVNFDQYEPIDQLNLVEEVSTKETVTYGEGSSHVVLID 173

Query: 177 FGMKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGV 236
           FG K  I+  L K  C V VVPY+   E ++ LKPDGI+LSNGPG+PK +   +  IK +
Sbjct: 174 FGYKKSIVDTLVKFDCKVTVVPYDTPFETIVTLKPDGILLSNGPGNPKQMAAQLNDIKKL 233

Query: 237 LGKVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTV--S 294
               P FGICLGHQL ALA GA+TEK++FGHRG+N PV++L T +V +TSQNH Y V  +
Sbjct: 234 AATYPTFGICLGHQLLALAFGADTEKLRFGHRGANQPVQDLLTKRVYMTSQNHSYVVKEN 293

Query: 295 SISKTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMIETTE 354
           S+  T L   +  IND ++EGL H  LP  +VQ+HPEA PGP D+  +F  FI+ + +  
Sbjct: 294 SLQDTGLVARYKNINDGSVEGLIHTQLPVASVQFHPEAHPGPSDSEEIFSIFIKEMSSKR 353

Query: 355 KE 356
           +E
Sbjct: 354 RE 355


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: 377
Number of extensions: 13
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: 364
Length of database: 359
Length adjustment: 29
Effective length of query: 335
Effective length of database: 330
Effective search space:   110550
Effective search space used:   110550
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_075385892.1 BK574_RS23580 (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.2900119.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-143  464.2   0.3   1.6e-143  464.0   0.3    1.0  1  NCBI__GCF_002019605.1:WP_075385892.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_075385892.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.0   0.3  1.6e-143  1.6e-143       2     360 ..       4     350 ..       3     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.0 bits;  conditional E-value: 1.6e-143
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                           +lvl+ G++feg+ +g+e +v+GevvF T+mtGYqE++tDps+kgqivv+typlignygvn+ d+esk+++v+
  NCBI__GCF_002019605.1:WP_075385892.1   4 YLVLSTGETFEGEWVGQEVDVYGEVVFFTGMTGYQEVITDPSFKGQIVVFTYPLIGNYGVNDFDNESKHPQVS 76 
                                           89*********************************************************************** PP

                             TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespk 147
                                           g++++e++ +  +y++k+s+++ +++++i+ ++g+DTRa+vk++Re g m a+i+t+ s+     +  ++ + 
  NCBI__GCF_002019605.1:WP_075385892.1  77 GVIMSECNPSGFHYESKQSFQDNCESSNIPMLTGIDTRAVVKRIRELGDMGAIITTDLSRV----N-FDQYEP 144
                                           *******************************************************999544....2.445567 PP

                             TIGR01368 148 vkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220
                                           ++++nlv+evstke++++ +     g++ +vv+id+G+K++i+++Lvk +++vtvvp+dt++e+i +l+pdgi
  NCBI__GCF_002019605.1:WP_075385892.1 145 IDQLNLVEEVSTKETVTYGE-----GSS-HVVLIDFGYKKSIVDTLVKFDCKVTVVPYDTPFETIVTLKPDGI 211
                                           7789**************94.....444.7******************************************* PP

                             TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveits 293
                                           llsnGPG+P+++ ++++ +kkl+  ++P+fGIclGhqllala+ga+t kl+fGhrGaN+pv+dl t+rv++ts
  NCBI__GCF_002019605.1:WP_075385892.1 212 LLSNGPGNPKQMAAQLNDIKKLAA-TYPTFGICLGHQLLALAFGADTEKLRFGHRGANQPVQDLLTKRVYMTS 283
                                           ***********************9.************************************************ PP

                             TIGR01368 294 qNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                           qNH+y+v+e+sl+ + l ++ +n+nDg+vegl h++lpv svQ+HPea+pGp+d+e +F+ f+++++
  NCBI__GCF_002019605.1:WP_075385892.1 284 QNHSYVVKENSLQDTGLVARYKNINDGSVEGLIHTQLPVASVQFHPEAHPGPSDSEEIFSIFIKEMS 350
                                           ***************************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (359 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: 18.34
//
[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