Alignments for a candidate for carA in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Sphingomonas koreensis DSMZ 15582

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate Ga0059261_0006 Ga0059261_0006 carbamoyl-phosphate synthase, small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Korea:Ga0059261_0006
          Length = 390

 Score =  379 bits (973), Expect = e-110
 Identities = 199/376 (52%), Positives = 249/376 (66%), Gaps = 4/376 (1%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           + +LVL  G    GR  GA G A GEV F+T+MTGYQEI+TDPS++ Q++  T+PHIGNV
Sbjct: 14  TGVLVLASGEVIWGRGFGAEGHAAGEVCFHTAMTGYQEIMTDPSFAGQMICFTFPHIGNV 73

Query: 64  GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123
           G N  D E+   HA G+++R+     SNFR+ E L  ++K+H+ + +A IDTR LTR +R
Sbjct: 74  GANPDDVEADNPHALGMIVREDVTEPSNFRSVERLDDWMKQHDRIGLAGIDTRALTRRIR 133

Query: 124 EKGAQNGCII--AGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGL 181
            +GA NG I   A    D    LE+ARA+PGL GMDLA  VTT   + W  G W L  G 
Sbjct: 134 GQGAPNGVIAHSASGEFDIPWLLERARAWPGLEGMDLAITVTTETHFGWEGGVWRLGFGY 193

Query: 182 PEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNG 241
            E   ED  P HVVA D+G+K NI R LV  G ++T++PA  +AE VL  NPDGIFLSNG
Sbjct: 194 GEEGAEDGRP-HVVAIDYGSKHNIFRNLVQAGAKVTVLPATATAEQVLSFNPDGIFLSNG 252

Query: 242 PGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           PGDPA   +YA+  I++ LET  P+FGICLGHQLL LA GA+T KM  GH G NHPVK +
Sbjct: 253 PGDPAATGEYAVPVIRELLETKKPLFGICLGHQLLGLAVGAQTTKMFQGHRGANHPVKRL 312

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
               V IT+ NHGFA+D ATLPAN+  TH SLFDG+  GI      AFS Q HPEASPGP
Sbjct: 313 SDGAVEITSMNHGFAIDRATLPANVTETHVSLFDGSNCGIEIDGGRAFSVQYHPEASPGP 372

Query: 361 HDAAPLFDHFIELIEQ 376
            D+  LF+ F+ ++ Q
Sbjct: 373 QDSFYLFERFVGMLGQ 388


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: 475
Number of extensions: 22
Number of successful extensions: 4
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: 390
Length adjustment: 30
Effective length of query: 352
Effective length of database: 360
Effective search space:   126720
Effective search space used:   126720
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 Ga0059261_0006 Ga0059261_0006 (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.2037.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-131  424.3   0.0   2.2e-131  424.1   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0006  Ga0059261_0006 carbamoyl-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0006  Ga0059261_0006 carbamoyl-phosphate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.1   0.0  2.2e-131  2.2e-131       2     358 ..      16     385 ..      15     388 .. 0.95

  Alignments for each domain:
  == domain 1  score: 424.1 bits;  conditional E-value: 2.2e-131
                                 TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskk 70 
                                               +lvl+ G+v+ g++fgae++++Gev+F+T+mtGYqEi+tDps++gq++ +t p+ign+g n++d+e+++
  lcl|FitnessBrowser__Korea:Ga0059261_0006  16 VLVLASGEVIWGRGFGAEGHAAGEVCFHTAMTGYQEIMTDPSFAGQMICFTFPHIGNVGANPDDVEADN 84 
                                               69******************************************************************* PP

                                 TIGR01368  71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...ke 136
                                               +++ g++v+e  +e+sn+r+ e L++++k+++ ++++g+DTRal++++R +g+ ++vi++++s      
  lcl|FitnessBrowser__Korea:Ga0059261_0006  85 PHALGMIVREDVTEPSNFRSVERLDDWMKQHDRIGLAGIDTRALTRRIRGQGAPNGVIAHSASGefdIP 153
                                               ***********************************************************9987744455 PP

                                 TIGR01368 137 elvekakespkvkevnlvkevstkeayeleq..........kakkegkklrvvvidlGvKenilreLvk 195
                                                l e+a++ p +++++l+ +v+t+++  +e           ++ +e+ + +vv+id+G K+ni r+Lv+
  lcl|FitnessBrowser__Korea:Ga0059261_0006 154 WLLERARAWPGLEGMDLAITVTTETHFGWEGgvwrlgfgygEEGAEDGRPHVVAIDYGSKHNIFRNLVQ 222
                                               6889999**********************9988877766653555566679****************** PP

                                 TIGR01368 196 rgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalal 263
                                                g++vtv+pa+++ae++ ++npdgi+lsnGPGdPaa  e+a+  +++lle+k+P+fGIclGhqll+la+
  lcl|FitnessBrowser__Korea:Ga0059261_0006 223 AGAKVTVLPATATAEQVLSFNPDGIFLSNGPGDPAATgEYAVPVIRELLETKKPLFGICLGHQLLGLAV 291
                                               **********************************876377899************************** PP

                                 TIGR01368 264 gaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpv 332
                                               ga+t k+  GhrGaNhpvk l++g veits NHg+a+d+++l+++ ++ thv+l+Dg++ g+e    ++
  lcl|FitnessBrowser__Korea:Ga0059261_0006 292 GAQTTKMFQGHRGANHPVKRLSDGAVEITSMNHGFAIDRATLPAN-VTETHVSLFDGSNCGIEIDGGRA 359
                                               *****************************************8866.99********************* PP

                                 TIGR01368 333 fsvQyHPeaspGphdteylFdefvel 358
                                               fsvQyHPeaspGp+d+ ylF++fv +
  lcl|FitnessBrowser__Korea:Ga0059261_0006 360 FSVQYHPEASPGPQDSFYLFERFVGM 385
                                               ***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (390 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: 00:00:00.01
# Mc/sec: 7.84
//
[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