Alignments for a candidate for carA in Sphingomonas indica Dd16

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Sphingomonas indica Dd16

Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_085218731.1 B9N75_RS10355 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= curated2:Q92N95
         (401 letters)



>NCBI__GCF_900177405.1:WP_085218731.1
          Length = 415

 Score =  447 bits (1149), Expect = e-130
 Identities = 228/406 (56%), Positives = 279/406 (68%), Gaps = 30/406 (7%)

Query: 13  TALLVLADGTVIEGKGIGATGTVQAEVCFNTALTGYQEILTDPSYLGQIVTFTFPHIGNI 72
           T +LVLADGT++ GKG GA G    EVCFNTA+TGYQE++TDPSY  QI+TFTFPHIGN+
Sbjct: 14  TGVLVLADGTIVWGKGFGAEGDAVGEVCFNTAMTGYQEVMTDPSYAAQIITFTFPHIGNV 73

Query: 73  GANDEDIEDLTPAARHGAVGVIFKADITEPSNYRAAKHLDAWLKARGIIGLCGIDTRALT 132
           GAN ED+E   P A    +G I + D+T PSN+RAA     W+++ G IGL G+DTRALT
Sbjct: 74  GANYEDVEADNPHA----LGCIVRQDVTAPSNFRAATGFVEWMRSNGRIGLAGVDTRALT 129

Query: 133 AWIRENGMPNAVIAHDPAGVFDVEALKAEAKAWSGLEGLDLAKVATSGQSYRWNEKPWVW 192
             IR  G P  VIAH+  G FD++AL  +A++W GLEG+DLAK  +  Q YRW+   W  
Sbjct: 130 RRIRLAGAPTGVIAHNAGGEFDIDALLEKARSWPGLEGMDLAKEVSCRQMYRWSGGLWKL 189

Query: 193 NEGYST--------LGE--TDAAY----------------HVVALDYGVKRNILRLFAGL 226
            EGY          LGE  +DA+                 H+VA+DYG KRNI R  A  
Sbjct: 190 GEGYEEFPSREREGLGEGLSDASTSSPPAPPANGRRGDLPHIVAIDYGSKRNIFRNLADA 249

Query: 227 NCRVTVVPAQTSAEEVLALKPDGIFLSNGPGDPAATGEYAVPVIQDLLKTDIPVFGICLG 286
             RVTV+PA  + +EV+   PDG FLSNGPGDPAATG YAVPVI+ +L+T  P+FGICLG
Sbjct: 250 GARVTVLPATATFDEVMTHAPDGFFLSNGPGDPAATGAYAVPVIRQMLETGKPLFGICLG 309

Query: 287 HQMLALALGARTEKMHQGHHGANHPVKDHTTGKVEIVSMNHGFAVDANSLPQGVEQTHIS 346
           HQ+L LA+GA+T KMHQGH GANHPVK    G+VEI SMNHGFAV+A SLP     TH+S
Sbjct: 310 HQLLGLAVGAKTVKMHQGHRGANHPVKRLADGRVEITSMNHGFAVEAESLPANARPTHVS 369

Query: 347 LFDGTNCGLRVDGRPVFSVQHHPEASPGPQDSHYLFRRFLNLIREK 392
           LFDG+  GL +  RP FSVQ+HPEASPGPQDS YLF +F+ +I E+
Sbjct: 370 LFDGSLAGLELTDRPAFSVQYHPEASPGPQDSVYLFGKFVEMIGEE 415


Lambda     K      H
   0.318    0.136    0.417 

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: 561
Number of extensions: 24
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: 401
Length of database: 415
Length adjustment: 31
Effective length of query: 370
Effective length of database: 384
Effective search space:   142080
Effective search space used:   142080
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_085218731.1 B9N75_RS10355 (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.1649741.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-131  422.3   0.0     1e-130  421.9   0.0    1.1  1  NCBI__GCF_900177405.1:WP_085218731.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085218731.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.9   0.0    1e-130    1e-130       2     359 ..      16     412 ..      15     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 421.9 bits;  conditional E-value: 1e-130
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                           +lvl+dGt++ gk+fgae+++vGev+FnT+mtGYqE++tDpsY+ qi+++t p+ign+g n ed+e++++++ 
  NCBI__GCF_900177405.1:WP_085218731.1  16 VLVLADGTIVWGKGFGAEGDAVGEVCFNTAMTGYQEVMTDPSYAAQIITFTFPHIGNVGANYEDVEADNPHAL 88 
                                           69*********************************************************************** PP

                             TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelvekake 144
                                           g +v++  +++sn+ra + + e+++++g ++++gvDTRal++++R +g+ ++vi++++      + l eka++
  NCBI__GCF_900177405.1:WP_085218731.1  89 GCIVRQDVTAPSNFRAATGFVEWMRSNGRIGLAGVDTRALTRRIRLAGAPTGVIAHNAGGefdIDALLEKARS 161
                                           *******************************************************9875444489999***** PP

                             TIGR01368 145 spkvkevnlvkevstkeayeleq............................k........akkegkklrvvvi 181
                                            p +++++l+kevs+++ y+++                             +        + ++g+  ++v+i
  NCBI__GCF_900177405.1:WP_085218731.1 162 WPGLEGMDLAKEVSCRQMYRWSGglwklgegyeefpsrereglgeglsdasTssppappaNGRRGDLPHIVAI 234
                                           **********************99999999999998888877777666655056666665555666689**** PP

                             TIGR01368 182 dlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIc 253
                                           d+G K+ni r+L++ g++vtv+pa+++++e+++  pdg +lsnGPGdPaa   +a+  ++++le+ +P+fGIc
  NCBI__GCF_900177405.1:WP_085218731.1 235 DYGSKRNIFRNLADAGARVTVLPATATFDEVMTHAPDGFFLSNGPGDPAATgAYAVPVIRQMLETGKPLFGIC 307
                                           ************************************************8772678999*************** PP

                             TIGR01368 254 lGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtvegle 326
                                           lGhqll+la+gakt+k++ GhrGaNhpvk l++grveits NHg+av+ esl+++ +++thv+l+Dg+++gle
  NCBI__GCF_900177405.1:WP_085218731.1 308 LGHQLLGLAVGAKTVKMHQGHRGANHPVKRLADGRVEITSMNHGFAVEAESLPAN-ARPTHVSLFDGSLAGLE 379
                                           ***************************************************9866.9**************** PP

                             TIGR01368 327 hkelpvfsvQyHPeaspGphdteylFdefveli 359
                                            ++ p+fsvQyHPeaspGp+d+ ylF +fve+i
  NCBI__GCF_900177405.1:WP_085218731.1 380 LTDRPAFSVQYHPEASPGPQDSVYLFGKFVEMI 412
                                           ******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (415 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: 16.37
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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