Alignments for a candidate for carA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Desulfovibrio vulgaris Miyazaki F

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate 8501652 DvMF_2370 carbamoyl phosphate synthase small subunit (RefSeq)

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__Miya:8501652
          Length = 376

 Score =  315 bits (808), Expect = 1e-90
 Identities = 163/374 (43%), Positives = 237/374 (63%), Gaps = 8/374 (2%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L LEDG +   +SF   G    E++FNT +TGYQE+LTDPSYAGQ V MT P IGN G
Sbjct: 3   AFLALEDGFVLEGRSFTGRGESGGEVIFNTGMTGYQEVLTDPSYAGQMVCMTYPLIGNYG 62

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           V  +D ESG+  +   +++    + SNWR   +L DYL +  +MG+  +DTRA+TR LR 
Sbjct: 63  VTAEDMESGKVHVEAFIVKECCRTPSNWRAIMSLPDYLAQHGVMGIEGIDTRALTRHLRI 122

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSWDIV-GIDLISDVSCKSPYEWVDKTNAE----WDF 232
           +G++ G++STE +   DEL++ +R+   + G +L++ V+  +PY W D T  +       
Sbjct: 123 NGAMRGIISTE-TDDRDELVRRARALPTMEGQNLVTRVAPATPYRW-DGTRPQPVQLAAD 180

Query: 233 NTNSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGP 292
              +  G   +++ YD+GIK NILR L+  G  + VVP +F A +      + +  SNGP
Sbjct: 181 GAYAWPGTGPRLVVYDYGIKWNILRLLTDQGFDLLVVPPSFTAMQVAASGAEAVFLSNGP 240

Query: 293 GDPSAVPYAVETVKELLGKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRTG 352
           GDP+ +   V  ++ +  ++PV GIC+GHQLLG ALGG T K+KFGHHG NHPV++  TG
Sbjct: 241 GDPATLTDEVREIRVMTERMPVAGICLGHQLLGHALGGTTHKLKFGHHGCNHPVKDLVTG 300

Query: 353 QVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHDS 412
            +EIS+QNH + VD  S+P  VE+THVNLNDG+  G +     ++++Q+HPEASPGP DS
Sbjct: 301 HIEISSQNHGFCVDIESVP-DVEITHVNLNDGTLEGFAHKTRPILAVQHHPEASPGPTDS 359

Query: 413 DNAFREFIELMKRS 426
              F  F  +++ +
Sbjct: 360 RYFFARFRGMVREA 373


Lambda     K      H
   0.316    0.134    0.403 

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: 498
Number of extensions: 25
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: 430
Length of database: 376
Length adjustment: 31
Effective length of query: 399
Effective length of database: 345
Effective search space:   137655
Effective search space used:   137655
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: 50 (23.9 bits)

Align candidate 8501652 DvMF_2370 (carbamoyl phosphate synthase small subunit (RefSeq))
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.28574.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-142  460.9   0.0   1.5e-142  460.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501652  DvMF_2370 carbamoyl phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501652  DvMF_2370 carbamoyl phosphate synthase small subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.7   0.0  1.5e-142  1.5e-142       2     360 ..       4     371 ..       3     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 460.7 bits;  conditional E-value: 1.5e-142
                         TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvv 78 
                                        l+ledG v+eg+sf  ++e  Gev+FnT+mtGYqE+ltDpsY+gq+v +typlignygv++ed+es k++v++++v
  lcl|FitnessBrowser__Miya:8501652   4 FLALEDGFVLEGRSFTGRGESGGEVIFNTGMTGYQEVLTDPSYAGQMVCMTYPLIGNYGVTAEDMESGKVHVEAFIV 80 
                                       79*************************************************************************** PP

                         TIGR01368  79 kelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespkvkevnlvk 155
                                       ke+++++sn+ra  sL ++l+++g+++ieg+DTRal+++lR +g+m+++iste+ +++elv++a++ p+++++nlv+
  lcl|FitnessBrowser__Miya:8501652  81 KECCRTPSNWRAIMSLPDYLAQHGVMGIEGIDTRALTRHLRINGAMRGIISTETDDRDELVRRARALPTMEGQNLVT 157
                                       ***************************************************************************** PP

                         TIGR01368 156 evstkeayeleq......k......akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220
                                       +v+ +++y++        +          g+  r+vv+d+G+K nilr L+++g+++ vvp +++a ++++   +++
  lcl|FitnessBrowser__Miya:8501652 158 RVAPATPYRWDGtrpqpvQlaadgaYAWPGTGPRLVVYDYGIKWNILRLLTDQGFDLLVVPPSFTAMQVAASGAEAV 234
                                       **********997776661555565555666679******************************************* PP

                         TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHg 297
                                       +lsnGPGdPa++++ +++++ ++e ++P+ GIclGhqll+ alg+ t+klkfGh+G Nhpvkdl tg++ei+sqNHg
  lcl|FitnessBrowser__Miya:8501652 235 FLSNGPGDPATLTDEVREIRVMTE-RMPVAGICLGHQLLGHALGGTTHKLKFGHHGCNHPVKDLVTGHIEISSQNHG 310
                                       *********************999.**************************************************** PP

                         TIGR01368 298 yavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                       + vd es++  ++e+thvnlnDgt+eg +hk+ p+++vQ+HPeaspGp+d++y+F +f  +++
  lcl|FitnessBrowser__Miya:8501652 311 FCVDIESVP--DVEITHVNLNDGTLEGFAHKTRPILAVQHHPEASPGPTDSRYFFARFRGMVR 371
                                       *******87..79*********************************************88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (376 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: 11.74
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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