Alignments for a candidate for carA in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Acidimicrobium ferrooxidans DSM 10331

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_015799095.1 AFER_RS08805 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000023265.1:WP_015799095.1
          Length = 381

 Score =  245 bits (626), Expect = 1e-69
 Identities = 154/381 (40%), Positives = 207/381 (54%), Gaps = 29/381 (7%)

Query: 5   ALLVLEDGTQFHGRAIGATG------SAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYP 58
           A LVL  G +F G  +   G          EVVFNT+M+GY E +TDPSY  Q+V  T  
Sbjct: 13  AWLVLRSGARFRGAVVIPAGVEPLLDDVEAEVVFNTAMSGYVEAITDPSYYGQMVCFTTA 72

Query: 59  HIGNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKL 118
           H+G  G   AD +S +     ++     ++ASN      L+++L    +    D D+R+L
Sbjct: 73  HLGTYGVRRADVQSVRPWVSAVLAPRYSVVASNHAADTTLAAWLWEARVPLFVDFDSRRL 132

Query: 119 TRLLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLT 178
            RL+R  GA+ G I  GD PDAA   E+ R   G  G DL + VT  E            
Sbjct: 133 VRLVRAAGAEPGIITTGD-PDAAA--ERVRVAVGTEGRDLVRAVTRREPRELE------- 182

Query: 179 GGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRG-CRLTIVPAQTSAEDVLKMNPDGIF 237
              P        P  +VA DFG K  +L  L  RG  RL +VPA    E++ K++P  +F
Sbjct: 183 ---PLGHARSSRP--IVAIDFGVKERMLETL--RGPWRLVVVPATIRLEELEKLDPLAVF 235

Query: 238 LSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPV 297
           LSNGPGDPA     I  ++  L   +P+ GICLGHQLLALA+GA+T+K+ FGHHG NHPV
Sbjct: 236 LSNGPGDPAALTGPIELVRSLLGV-VPIAGICLGHQLLALAAGAETIKLPFGHHGSNHPV 294

Query: 298 KDVEKNVVMITAQNHGFAVDEAT---LPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHP 354
           +  E   V ITAQNH +AVDEA+   L     VT ++LFDG ++G+      A S Q HP
Sbjct: 295 RLEETGRVAITAQNHSYAVDEASLGRLDTPAEVTRRNLFDGVVEGLRLPALGAVSVQYHP 354

Query: 355 EASPGP-HDAAPLFDHFIELI 374
           EA+PGP   ++ + D  + L+
Sbjct: 355 EAAPGPLEQSSEIHDELLSLL 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: 388
Number of extensions: 17
Number of successful extensions: 5
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: 381
Length adjustment: 30
Effective length of query: 352
Effective length of database: 351
Effective search space:   123552
Effective search space used:   123552
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_015799095.1 AFER_RS08805 (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.8537.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-104  333.7   0.0   7.3e-104  333.5   0.0    1.0  1  lcl|NCBI__GCF_000023265.1:WP_015799095.1  AFER_RS08805 carbamoyl-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023265.1:WP_015799095.1  AFER_RS08805 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.5   0.0  7.3e-104  7.3e-104      20     356 ..      38     372 ..      13     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 333.5 bits;  conditional E-value: 7.3e-104
                                 TIGR01368  20 kevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvvkelskevsny 88 
                                                +v +evvFnT+m+GY E++tDpsY gq+v +t+ ++g ygv++ d++s +++v++++   +s  +sn+
  lcl|NCBI__GCF_000023265.1:WP_015799095.1  38 DDVEAEVVFNTAMSGYVEAITDPSYYGQMVCFTTAHLGTYGVRRADVQSVRPWVSAVLAPRYSVVASNH 106
                                               46789**************************************************************** PP

                                 TIGR01368  89 rakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlvkev 157
                                                a ++L+++l e  ++   + D R lv+ +R +g+  ++i+t +   + ++e+++++  +++ +lv+ v
  lcl|NCBI__GCF_000023265.1:WP_015799095.1 107 AADTTLAAWLWEARVPLFVDFDSRRLVRLVRAAGAEPGIITTGD--PDAAAERVRVAVGTEGRDLVRAV 173
                                               *******************************************9..6678888999999999******* PP

                                 TIGR01368 158 stkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsnGP 226
                                               + +e+ ele    +  +++ +v+id+GvKe +l++L     +++vvpa+ ++ee++kl+p +++lsnGP
  lcl|NCBI__GCF_000023265.1:WP_015799095.1 174 TRREPRELEPL-GHARSSRPIVAIDFGVKERMLETLR-GPWRLVVVPATIRLEELEKLDPLAVFLSNGP 240
                                               ********973.33334458*************9996.579**************************** PP

                                 TIGR01368 227 GdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqN 295
                                               GdPaa++  ie v++ll+  +Pi GIclGhqllala+ga+t+kl fGh+G+Nhpv+  +tgrv it+qN
  lcl|NCBI__GCF_000023265.1:WP_015799095.1 241 GDPAALTGPIELVRSLLG-VVPIAGICLGHQLLALAAGAETIKLPFGHHGSNHPVRLEETGRVAITAQN 308
                                               ******************.************************************************** PP

                                 TIGR01368 296 Hgyavdeesl..keeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphd.teylFdefv 356
                                               H+yavde+sl    + +evt +nl+Dg vegl+   l ++svQyHPea+pGp + ++ + de++
  lcl|NCBI__GCF_000023265.1:WP_015799095.1 309 HSYAVDEASLgrLDTPAEVTRRNLFDGVVEGLRLPALGAVSVQYHPEAAPGPLEqSSEIHDELL 372
                                               *********83345779***********************************762566777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (381 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.92
//
[ok]

This GapMind analysis is from Apr 10 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