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_078430671.1 BK574_RS26020 carbamoyl phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_002019605.1:WP_078430671.1
          Length = 362

 Score =  501 bits (1291), Expect = e-147
 Identities = 241/353 (68%), Positives = 284/353 (80%), Gaps = 2/353 (0%)

Query: 1   MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60
           MKR+L+LE+G VF G+AFGS     GEVVFNTGMTGYQEILSDPSYC QIVTLTYPLIGN
Sbjct: 1   MKRQLILEDGTVFVGKAFGSEHEKEGEVVFNTGMTGYQEILSDPSYCAQIVTLTYPLIGN 60

Query: 61  YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120
           YGINRDDFESI P + GLI+KE    PSNWR   ++D+ LK K IPGL+GIDTRKLTR+I
Sbjct: 61  YGINRDDFESIEPAIHGLIVKEAAIYPSNWRCEESIDDLLKAKGIPGLEGIDTRKLTRLI 120

Query: 121 RTAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFGMK 180
           R  G L+G   S + ++E V+K LN  E P +QV +VS K  Y  PGRG R+VLVDFG K
Sbjct: 121 RKHGTLRGRLCSMEVNVEEVVKELNAAEEPNDQVKRVSTKDPYHCPGRGHRVVLVDFGAK 180

Query: 181 HGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLGKV 240
           HGI++ L +R CDVIVVPYN +AEE+L+L PDGIMLSNGPG+P DVPE IEMIKG+LGKV
Sbjct: 181 HGIIQNLIQRDCDVIVVPYNTSAEEILRLYPDGIMLSNGPGNPVDVPEGIEMIKGLLGKV 240

Query: 241 PLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTV--SSISK 298
           P+FGICLGHQL ALACGA + K+ FGHRGSNHPV+EL TGK+ +TSQNHGYT+   S+  
Sbjct: 241 PIFGICLGHQLLALACGAKSAKLTFGHRGSNHPVRELETGKIDITSQNHGYTIEKDSLED 300

Query: 299 TELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMIE 351
           T L VTHIA+ND+T+EG+ H   PAF+VQYHPEASPGPED+NHLF +FI +IE
Sbjct: 301 TRLIVTHIAVNDETVEGVAHLDYPAFSVQYHPEASPGPEDSNHLFTKFINLIE 353


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: 509
Number of extensions: 18
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: 362
Length adjustment: 29
Effective length of query: 335
Effective length of database: 333
Effective search space:   111555
Effective search space used:   111555
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_078430671.1 BK574_RS26020 (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.984943.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-148  480.9   0.0   1.3e-148  480.7   0.0    1.0  1  NCBI__GCF_002019605.1:WP_078430671.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430671.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.7   0.0  1.3e-148  1.3e-148       2     360 ..       4     353 ..       3     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 480.7 bits;  conditional E-value: 1.3e-148
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                           +l+ledGtvf gk+fg+e+e+ GevvFnT+mtGYqEil+DpsY  qiv+ltyplignyg+n++d+es ++ ++
  NCBI__GCF_002019605.1:WP_078430671.1   4 QLILEDGTVFVGKAFGSEHEKEGEVVFNTGMTGYQEILSDPSYCAQIVTLTYPLIGNYGINRDDFESIEPAIH 76 
                                           699********************************************************************** PP

                             TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespk 147
                                           gl+vke++  +sn+r++es+++ lk +gi+++eg+DTR+l++ +R++g++++++ + +++ ee v++++++++
  NCBI__GCF_002019605.1:WP_078430671.1  77 GLIVKEAAIYPSNWRCEESIDDLLKAKGIPGLEGIDTRKLTRLIRKHGTLRGRLCSMEVNVEEVVKELNAAEE 149
                                           ******************************************************************9999999 PP

                             TIGR01368 148 vkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220
                                            +  + vk+vstk++y++        + +rvv++d+G K+ i+++L++r+++v+vvp++tsaeei +l+pdgi
  NCBI__GCF_002019605.1:WP_078430671.1 150 PN--DQVKRVSTKDPYHCPG------RGHRVVLVDFGAKHGIIQNLIQRDCDVIVVPYNTSAEEILRLYPDGI 214
                                           97..99**********9994......4457******************************************* PP

                             TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveits 293
                                           +lsnGPG+P +v e ie++k ll+ k+PifGIclGhqllala gak  kl fGhrG+Nhpv++l+tg+++its
  NCBI__GCF_002019605.1:WP_078430671.1 215 MLSNGPGNPVDVPEGIEMIKGLLG-KVPIFGICLGHQLLALACGAKSAKLTFGHRGSNHPVRELETGKIDITS 286
                                           ************************.************************************************ PP

                             TIGR01368 294 qNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                           qNHgy+++++sl+ ++l vth  +nD+tveg++h ++p+fsvQyHPeaspGp+d+++lF +f++li+
  NCBI__GCF_002019605.1:WP_078430671.1 287 QNHGYTIEKDSLEDTRLIVTHIAVNDETVEGVAHLDYPAFSVQYHPEASPGPEDSNHLFTKFINLIE 353
                                           ****************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (362 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.55
//
[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