Alignments for a candidate for carA in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Hydrogenophaga taeniospiralis NBRC 102512

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_068166058.1 HTA01S_RS00070 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_001592305.1:WP_068166058.1
          Length = 386

 Score =  491 bits (1265), Expect = e-143
 Identities = 245/379 (64%), Positives = 288/379 (75%), Gaps = 9/379 (2%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           ALL L DGT F G +IGATG   GEVVFNT++TGYQEILTDPSY +QIVTLTYPHIGN G
Sbjct: 8   ALLALADGTVFTGISIGATGQTTGEVVFNTALTGYQEILTDPSYCQQIVTLTYPHIGNTG 67

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            N  D E+++VHA GL+I+DLPL+ASNFR+ E LS YL+R   VAIAD+DTR LTR LR 
Sbjct: 68  VNREDVEATRVHAAGLIIKDLPLLASNFRSEETLSHYLQREGTVAIADLDTRALTRRLRT 127

Query: 125 KGAQNGCIIA---GDN---PDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLT 178
            GAQNGCI+A   G++      A AL  A+A P + G DLAK V+  E Y+WTQ  W L 
Sbjct: 128 HGAQNGCILALAPGESITDEHRARALAAAQAAPNMAGQDLAKVVSAREPYAWTQTEWQLG 187

Query: 179 GGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFL 238
            G  E   +    FHVVAYDFG K NILRML  RGC++T+VPAQT A DV K+ P G+FL
Sbjct: 188 FGYGE---QIAPKFHVVAYDFGVKHNILRMLSARGCKITVVPAQTPASDVFKLKPSGVFL 244

Query: 239 SNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK 298
           SNGPGDP PCDYAI A ++ +++ +P FGICLGHQ++ALASGAKT KMKFGHHG NHPVK
Sbjct: 245 SNGPGDPEPCDYAIAATREIIDSGVPTFGICLGHQIMALASGAKTFKMKFGHHGANHPVK 304

Query: 299 DVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358
           D++   V IT+QNHGFAVDE  LPA LR TH SLFDGTLQG+ RTD+PAF FQGHPEASP
Sbjct: 305 DLDSGRVSITSQNHGFAVDEKDLPATLRATHVSLFDGTLQGLARTDRPAFCFQGHPEASP 364

Query: 359 GPHDAAPLFDHFIELIEQY 377
           GPHD   LFD FIEL++++
Sbjct: 365 GPHDIGYLFDRFIELMQKH 383


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: 506
Number of extensions: 18
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: 382
Length of database: 386
Length adjustment: 30
Effective length of query: 352
Effective length of database: 356
Effective search space:   125312
Effective search space used:   125312
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_068166058.1 HTA01S_RS00070 (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.27475.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-145  471.1   0.0   1.3e-145  470.9   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068166058.1  HTA01S_RS00070 carbamoyl-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068166058.1  HTA01S_RS00070 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.9   0.0  1.3e-145  1.3e-145       1     361 []       8     382 ..       8     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 470.9 bits;  conditional E-value: 1.3e-145
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a l+l+dGtvf+g+s+ga+++++GevvFnT++tGYqEiltDpsY +qiv+ltyp+ign+gvn+ed+e++
  lcl|NCBI__GCF_001592305.1:WP_068166058.1   8 ALLALADGTVFTGISIGATGQTTGEVVFNTALTGYQEILTDPSYCQQIVTLTYPHIGNTGVNREDVEAT 76 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.... 134
                                               +++++gl++k+l   +sn+r++e+L+++l++eg vai+++DTRal+++lR++g+++++i + +      
  lcl|NCBI__GCF_001592305.1:WP_068166058.1  77 RVHAAGLIIKDLPLLASNFRSEETLSHYLQREGTVAIADLDTRALTRRLRTHGAQNGCILALAPGesit 145
                                               **********************************************************98755334455 PP

                                 TIGR01368 135 ...keelvekakespkvkevnlvkevstkeayeleq...k.....akkegkklrvvvidlGvKenilre 192
                                                  + ++ ++a+++p++++++l+k vs++e+y+++q   +      ++   k +vv++d+GvK+nilr+
  lcl|NCBI__GCF_001592305.1:WP_068166058.1 146 dehRARALAAAQAAPNMAGQDLAKVVSAREPYAWTQtewQlgfgyGEQIAPKFHVVAYDFGVKHNILRM 214
                                               5445667778889**********************9665166665667777899*************** PP

                                 TIGR01368 193 LvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllal 261
                                               L++rg+++tvvpa+t+a+++ kl+p+g++lsnGPGdP+ +++ai+ +++++++ +P+fGIclGhq++al
  lcl|NCBI__GCF_001592305.1:WP_068166058.1 215 LSARGCKITVVPAQTPASDVFKLKPSGVFLSNGPGDPEPCDYAIAATREIIDSGVPTFGICLGHQIMAL 283
                                               ********************************************************************* PP

                                 TIGR01368 262 algaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkel 330
                                               a+gakt+k+kfGh+GaNhpvkdl++grv+itsqNHg+avde+ l+++ l++thv+l+Dgt++gl++++ 
  lcl|NCBI__GCF_001592305.1:WP_068166058.1 284 ASGAKTFKMKFGHHGANHPVKDLDSGRVSITSQNHGFAVDEKDLPAT-LRATHVSLFDGTLQGLARTDR 351
                                               *******************************************8866.********************* PP

                                 TIGR01368 331 pvfsvQyHPeaspGphdteylFdefvelikk 361
                                               p+f  Q HPeaspGphd  ylFd+f+el++k
  lcl|NCBI__GCF_001592305.1:WP_068166058.1 352 PAFCFQGHPEASPGPHDIGYLFDRFIELMQK 382
                                               ****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (386 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: 7.80
//
[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