Alignments for a candidate for carA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Desulfovibrio vulgaris Hildenborough

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 208631 DVU3113 carbamoyl-phosphate synthase, small subunit

Query= SwissProt::P25993
         (364 letters)



>MicrobesOnline__882:208631
          Length = 375

 Score =  328 bits (842), Expect = 1e-94
 Identities = 164/371 (44%), Positives = 229/371 (61%), Gaps = 23/371 (6%)

Query: 1   MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60
           M+  L LE+G V EG +F       GE +FNTGMTGYQE+L+DPSY GQ+V +TYPL+GN
Sbjct: 1   MRALLALEDGFVLEGRSFTGPGETGGEAIFNTGMTGYQEVLTDPSYAGQMVCMTYPLVGN 60

Query: 61  YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120
           YG+ R+D ES    V+  I+KE C++PSNWRS  +L +YLK   + G++GIDTR LTR +
Sbjct: 61  YGVTREDMESGKVHVEAFIVKECCKVPSNWRSEISLPDYLKRHGVMGIEGIDTRALTRHL 120

Query: 121 RTAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSP-------------- 166
           R  GA++G  ++ + D   +++R     LP  +   +  + A  +P              
Sbjct: 121 RIHGAMRGVISTQETDPARLVERARA--LPSMEGQNLVTRVAPAAPYRWDGERPQAVTLE 178

Query: 167 -------GRGKRIVLVDFGMKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNG 219
                  G+G R+V+ DFG+K  ILR L ++  D++VVP +  A +V  +    + LSNG
Sbjct: 179 PGGCAWVGKGPRLVVYDFGIKWNILRLLAQQGFDMLVVPPSFKAADVAAVGAQAVFLSNG 238

Query: 220 PGDPKDVPEAIEMIKGVLGKVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELAT 279
           PGDP  + + I  I  +    P  GICLGHQL   A G  T K+KFGH G NHPVK+L T
Sbjct: 239 PGDPATLKDEIAEIAKLAQTYPTAGICLGHQLLGHALGGRTMKLKFGHHGCNHPVKDLTT 298

Query: 280 GKVALTSQNHGYTVSSISKTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDA 339
           G++ ++SQNHG+ V   S T++E+TH+ +ND T+EG  HKT P   VQ+HPEASPGP D+
Sbjct: 299 GRIEISSQNHGFCVDIDSLTDVEITHVNLNDGTLEGFAHKTKPVIAVQHHPEASPGPNDS 358

Query: 340 NHLFDRFIEMI 350
            + F RF  M+
Sbjct: 359 RYFFARFRNMV 369


Lambda     K      H
   0.317    0.136    0.397 

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: 410
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: 364
Length of database: 375
Length adjustment: 30
Effective length of query: 334
Effective length of database: 345
Effective search space:   115230
Effective search space used:   115230
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 208631 DVU3113 (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.27196.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-144  467.1   0.0   2.1e-144  466.9   0.0    1.0  1  lcl|MicrobesOnline__882:208631  DVU3113 carbamoyl-phosphate synt


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208631  DVU3113 carbamoyl-phosphate synthase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.9   0.0  2.1e-144  2.1e-144       1     360 [.       3     370 ..       3     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 466.9 bits;  conditional E-value: 2.1e-144
                       TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvvk 79 
                                     a l+ledG v+eg+sf  ++e+ Ge +FnT+mtGYqE+ltDpsY+gq+v +typl+gnygv++ed+es k++v++++vk
  lcl|MicrobesOnline__882:208631   3 ALLALEDGFVLEGRSFTGPGETGGEAIFNTGMTGYQEVLTDPSYAGQMVCMTYPLVGNYGVTREDMESGKVHVEAFIVK 81 
                                     579**************************************************************************** PP

                       TIGR01368  80 elskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlvkevs 158
                                     e++k +sn+r++ sL ++lk++g+++ieg+DTRal+++lR +g+m++vist++++  +lve+a++ p+++++nlv++v+
  lcl|MicrobesOnline__882:208631  82 ECCKVPSNWRSEISLPDYLKRHGVMGIEGIDTRALTRHLRIHGAMRGVISTQETDPARLVERARALPSMEGQNLVTRVA 160
                                     ******************************************************************************* PP

                       TIGR01368 159 tkeayeleq...k........akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsnGP 226
                                      + +y++     +            gk  r+vv+d+G+K nilr L+++g+++ vvp +++a++++++  ++++lsnGP
  lcl|MicrobesOnline__882:208631 161 PAAPYRWDGerpQavtlepggCAWVGKGPRLVVYDFGIKWNILRLLAQQGFDMLVVPPSFKAADVAAVGAQAVFLSNGP 239
                                     *******99666155555666455555668************************************************* PP

                       TIGR01368 227 GdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeesl 305
                                     GdPa++++ i+++ kl++ ++P+ GIclGhqll+ alg++t+klkfGh+G Nhpvkdl+tgr+ei+sqNHg+ vd +sl
  lcl|MicrobesOnline__882:208631 240 GDPATLKDEIAEIAKLAQ-TYPTAGICLGHQLLGHALGGRTMKLKFGHHGCNHPVKDLTTGRIEISSQNHGFCVDIDSL 317
                                     ******************.***********************************************************6 PP

                       TIGR01368 306 keeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                     +  ++e+thvnlnDgt+eg +hk++pv++vQ+HPeaspGp+d++y+F +f ++++
  lcl|MicrobesOnline__882:208631 318 T--DVEITHVNLNDGTLEGFAHKTKPVIAVQHHPEASPGPNDSRYFFARFRNMVR 370
                                     6..89*********************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (375 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: 6.88
//
[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