Alignments for a candidate for carA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Pseudomonas stutzeri RCH2

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate GFF938 Psest_0967 carbamoyl-phosphate synthase, small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__psRCH2:GFF938
          Length = 382

 Score =  533 bits (1372), Expect = e-156
 Identities = 261/374 (69%), Positives = 299/374 (79%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           A+L L DG+ F G +IGA G  +GEVVFNT+MTGYQEILTDPSY++QIVTLTYPH+GN G
Sbjct: 9   AILALADGSIFRGESIGADGQTIGEVVFNTAMTGYQEILTDPSYAKQIVTLTYPHVGNTG 68

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
           T   D ES +V A GLVIRDLPLI+SN+R+ + L  YLK +  VAIA IDTR+LTR+LRE
Sbjct: 69  TTPEDAESWKVWAAGLVIRDLPLISSNWRDKQPLPDYLKANGTVAIAGIDTRRLTRILRE 128

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGAQNGCI+AG +     ALE AR+FPGL GMDLAKEV+  E Y W    W L       
Sbjct: 129 KGAQNGCILAGSDATEEKALELARSFPGLKGMDLAKEVSVKERYEWRSSVWCLKDDGHAE 188

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
               ELP+HVVA+D+G K NILRMLV RGCR+T++PAQT A + L +NPDGIFL+NGPGD
Sbjct: 189 IPASELPYHVVAFDYGVKYNILRMLVARGCRVTVLPAQTPASEALALNPDGIFLANGPGD 248

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           P PCDYAI AIQ+ LETDIPVFGICLGHQLLALASGAKTVKM  GHHG NHPV+D++  V
Sbjct: 249 PEPCDYAIKAIQEVLETDIPVFGICLGHQLLALASGAKTVKMPNGHHGANHPVQDLKTGV 308

Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364
           VMIT+QNHGFAVDEA+LPAN+R THKSLFDGTLQGI RTDK AFSFQGHPEASPGPHD A
Sbjct: 309 VMITSQNHGFAVDEASLPANVRATHKSLFDGTLQGIERTDKAAFSFQGHPEASPGPHDVA 368

Query: 365 PLFDHFIELIEQYR 378
           PLFD FIE + + R
Sbjct: 369 PLFDRFIETMAKRR 382


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: 527
Number of extensions: 10
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 GFF938 Psest_0967 (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.3164.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-145  470.7   0.0   1.7e-145  470.5   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF938  Psest_0967 carbamoyl-phosphate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF938  Psest_0967 carbamoyl-phosphate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.5   0.0  1.7e-145  1.7e-145       1     360 [.       9     379 ..       9     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 470.5 bits;  conditional E-value: 1.7e-145
                          TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkgl 76 
                                        a+l+l+dG++f+g+s+ga+++++GevvFnT+mtGYqEiltDpsY++qiv+ltyp++gn+g+++edaes k++++gl
  lcl|FitnessBrowser__psRCH2:GFF938   9 AILALADGSIFRGESIGADGQTIGEVVFNTAMTGYQEILTDPSYAKQIVTLTYPHVGNTGTTPEDAESWKVWAAGL 84 
                                        689************************************************************************* PP

                          TIGR01368  77 vvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvkev 151
                                        v+++l    sn+r k+ L ++lk +g vai+g+DTR l++ lRekg+++++i + + + +e++ e a++ p +k++
  lcl|FitnessBrowser__psRCH2:GFF938  85 VIRDLPLISSNWRDKQPLPDYLKANGTVAIAGIDTRRLTRILREKGAQNGCILAGSDAtEEKALELARSFPGLKGM 160
                                        ***************************************************99877653778889999******** PP

                          TIGR01368 152 nlvkevstkeayeleq.........k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikkln 216
                                        +l+kevs+ke+ye+++         +  + +++  ++vv++d+GvK nilr+Lv+rg++vtv+pa+t+a+e  +ln
  lcl|FitnessBrowser__psRCH2:GFF938 161 DLAKEVSVKERYEWRSsvwclkddgHaeIPASELPYHVVAFDYGVKYNILRMLVARGCRVTVLPAQTPASEALALN 236
                                        ***************977777665523344444449**************************************** PP

                          TIGR01368 217 pdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveit 292
                                        pdgi+l+nGPGdP+ +++ai+ ++++le++iP+fGIclGhqllala+gakt+k+  Gh+GaNhpv+dlktg v+it
  lcl|FitnessBrowser__psRCH2:GFF938 237 PDGIFLANGPGDPEPCDYAIKAIQEVLETDIPVFGICLGHQLLALASGAKTVKMPNGHHGANHPVQDLKTGVVMIT 312
                                        **************************************************************************** PP

                          TIGR01368 293 sqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                        sqNHg+avde+sl+++ +++th++l+Dgt++g+e++++++fs Q HPeaspGphd + lFd+f+e+++
  lcl|FitnessBrowser__psRCH2:GFF938 313 SQNHGFAVDEASLPAN-VRATHKSLFDGTLQGIERTDKAAFSFQGHPEASPGPHDVAPLFDRFIETMA 379
                                        ************8866.************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (382 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: 7.25
//
[ok]

This GapMind analysis is from Apr 09 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