Alignments for a candidate for carA in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Pseudomonas simiae WCS417

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate GFF4700 PS417_24045 carbamoyl phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__WCS417:GFF4700
          Length = 378

 Score =  531 bits (1368), Expect = e-155
 Identities = 260/378 (68%), Positives = 299/378 (79%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           M K A+L L DG+ F G AIGA G  VGEVVFNT+MTGYQEILTDPSY++QIVTLTYPHI
Sbjct: 1   MTKPAILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GN GT   D ES +V + GLVIRDLPL+ASN+RNT  LS YLK +N+VAIA IDTR+LTR
Sbjct: 61  GNTGTTPEDVESDRVWSAGLVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGIDTRRLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LREKG+QNGCI+ GDN     A+  A+ FPGL GMDLAK V+  E Y W    W L   
Sbjct: 121 ILREKGSQNGCIMVGDNISEEAAIAAAQGFPGLKGMDLAKVVSVKEKYEWRSTVWDLKTD 180

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
                   +LP+HVVAYD+G K NILRMLV+RGCR+T+VPAQT A DVL + PDG+FLSN
Sbjct: 181 SHATIDAADLPYHVVAYDYGVKYNILRMLVERGCRVTVVPAQTPASDVLALQPDGVFLSN 240

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDP PCDYAI AI+  LET+IPVFGICLGHQLLALASGAKT+KM  GHHG NHPV+D+
Sbjct: 241 GPGDPEPCDYAIQAIKDVLETEIPVFGICLGHQLLALASGAKTLKMGHGHHGANHPVQDL 300

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           +  VVMIT+QNHGFAVDEATLP+N+R  HKSLFDG+LQGI RTDK AFSFQGHPEASPGP
Sbjct: 301 DTGVVMITSQNHGFAVDEATLPSNVRAIHKSLFDGSLQGIERTDKSAFSFQGHPEASPGP 360

Query: 361 HDAAPLFDHFIELIEQYR 378
           +D APLFD FI  + + R
Sbjct: 361 NDVAPLFDRFINEMAKRR 378


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: 514
Number of extensions: 12
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: 378
Length adjustment: 30
Effective length of query: 352
Effective length of database: 348
Effective search space:   122496
Effective search space used:   122496
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 GFF4700 PS417_24045 (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.10912.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-147  477.0   0.0     2e-147  476.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4700  PS417_24045 carbamoyl phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4700  PS417_24045 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.8   0.0    2e-147    2e-147       1     360 [.       5     375 ..       5     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 476.8 bits;  conditional E-value: 2e-147
                           TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkg 75 
                                         a+l+l+dG++f+g+++ga++++vGevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+g+++ed+es++++ +g
  lcl|FitnessBrowser__WCS417:GFF4700   5 AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHIGNTGTTPEDVESDRVWSAG 79 
                                         689************************************************************************ PP

                           TIGR01368  76 lvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvk 149
                                         lv+++l   +sn+r++ sL+++lk +++vai+g+DTR l++ lRekgs++++i+  ++  +e ++++a+  p +k
  lcl|FitnessBrowser__WCS417:GFF4700  80 LVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGIDTRRLTRILREKGSQNGCIMVGDNIsEEAAIAAAQGFPGLK 154
                                         *****************************************************99875426778888999***** PP

                           TIGR01368 150 evnlvkevstkeayeleq.........k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeik 213
                                         +++l+k vs+ke+ye+++         +  + + +  ++vv++d+GvK nilr+Lv+rg++vtvvpa+t+a+++ 
  lcl|FitnessBrowser__WCS417:GFF4700 155 GMDLAKVVSVKEKYEWRStvwdlktdsHatIDAADLPYHVVAYDYGVKYNILRMLVERGCRVTVVPAQTPASDVL 229
                                         *****************977777655414344455559************************************* PP

                           TIGR01368 214 klnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgr 288
                                         +l+pdg++lsnGPGdP+ +++ai+ +k +le++iP+fGIclGhqllala+gakt+k+  Gh+GaNhpv+dl+tg 
  lcl|FitnessBrowser__WCS417:GFF4700 230 ALQPDGVFLSNGPGDPEPCDYAIQAIKDVLETEIPVFGICLGHQLLALASGAKTLKMGHGHHGANHPVQDLDTGV 304
                                         *************************************************************************** PP

                           TIGR01368 289 veitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                         v+itsqNHg+avde++l+++ +++ h++l+Dg+++g+e++++ +fs Q HPeaspGp+d + lFd+f+++++
  lcl|FitnessBrowser__WCS417:GFF4700 305 VMITSQNHGFAVDEATLPSN-VRAIHKSLFDGSLQGIERTDKSAFSFQGHPEASPGPNDVAPLFDRFINEMA 375
                                         ****************8866.************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (378 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.87
//
[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