Alignments for a candidate for leuA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Desulfovibrio vulgaris Miyazaki F

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate 8501055 DvMF_1791 2-isopropylmalate synthase (RefSeq)

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Miya:8501055
          Length = 514

 Score =  531 bits (1367), Expect = e-155
 Identities = 276/512 (53%), Positives = 364/512 (71%), Gaps = 3/512 (0%)

Query: 3   QTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNA 62
           ++ R+ IFDTTLRDGEQSPGA M  +EKIR+ARQLE LGVDI+EAGF A+S GDFEAV A
Sbjct: 4   ESGRIRIFDTTLRDGEQSPGATMNLQEKIRLARQLETLGVDIMEAGFPASSQGDFEAVQA 63

Query: 63  IAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIE 122
           IA+ +    V  L RA+  DI +A EAV  A   RIHTF+ATSP+HM+YKL+ +P QV+E
Sbjct: 64  IARAVKGVEVAGLCRAMPADIDRAWEAVKVAENPRIHTFLATSPVHMQYKLRKEPDQVVE 123

Query: 123 AAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKT 182
            AV AV+ A +YT +VEFS EDA RS  DFL  +  AVI AGATTIN+PDTVGY+ P + 
Sbjct: 124 MAVAAVRHAAKYTSNVEFSAEDASRSNPDFLVRVFEAVINAGATTINVPDTVGYAQPEEF 183

Query: 183 EEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNAS 242
               R +I  TPN  K V+S HCHNDLG+ VAN+LAALK GARQ E T++G+GERAGNAS
Sbjct: 184 GRLIRYVIENTPNSHKAVFSVHCHNDLGMGVANTLAALKAGARQAEVTISGIGERAGNAS 243

Query: 243 VEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIH 302
           +EEIVMAL  R D + L+ G+ T Q+ P+ +L+S I G P+ PNKAIVGANAF+HESGIH
Sbjct: 244 LEEIVMALHTRRDFYQLDCGVVTEQLFPTCRLLSMIIGQPIPPNKAIVGANAFAHESGIH 303

Query: 303 QDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFAR 362
           QDG+LK+RETYEIM+ ES+G     L +GK SGRNA K KL +LG  LE E  L   F  
Sbjct: 304 QDGMLKNRETYEIMTPESIGKTKTDLVIGKHSGRNAVKNKLDELGYRLE-EAQLVTVFEA 362

Query: 363 FKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKIS-TETGEEPRADIVFSIKGEE 421
            K+LADKK++I+DED+ ALV +E+  +  + Y+ ++  +  ++TG  P A +V  + GE 
Sbjct: 363 VKKLADKKKQIYDEDIEALVLEEVYRL-PDLYRLVNLSVQCSDTGMPPTAAVVMDVMGEV 421

Query: 422 KRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQ 481
           KRA+  G GP+DA+F  I  +      L+ YSV A+T GT++QGE +VRL +      G+
Sbjct: 422 KRAAGFGVGPIDAVFNVIGEIVGRAPVLERYSVTAITGGTDAQGEVTVRLRQNGSSAVGR 481

Query: 482 GADTDVLVATAKAYLSALSKLEFSAAKPKAQG 513
           G+D D+++A+A+AY++AL++L     + + +G
Sbjct: 482 GSDPDIILASARAYVNALNRLAKKEEEQEKEG 513


Lambda     K      H
   0.313    0.129    0.352 

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: 628
Number of extensions: 19
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: 517
Length of database: 514
Length adjustment: 35
Effective length of query: 482
Effective length of database: 479
Effective search space:   230878
Effective search space used:   230878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 8501055 DvMF_1791 (2-isopropylmalate synthase (RefSeq))
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.2954.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.5e-221  721.3   0.4   2.8e-221  721.1   0.4    1.0  1  lcl|FitnessBrowser__Miya:8501055  DvMF_1791 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501055  DvMF_1791 2-isopropylmalate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.1   0.4  2.8e-221  2.8e-221       1     494 []       7     500 ..       7     500 .. 0.99

  Alignments for each domain:
  == domain 1  score: 721.1 bits;  conditional E-value: 2.8e-221
                         TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekd 77 
                                       r+ ifdttlrdGeq+pga+++++ek+++a++le lgvdi+eaGfp+ss+gdfeavq iar+vk  +v+gl+ra+  d
  lcl|FitnessBrowser__Miya:8501055   7 RIRIFDTTLRDGEQSPGATMNLQEKIRLARQLETLGVDIMEAGFPASSQGDFEAVQAIARAVKGVEVAGLCRAMPAD 83 
                                       799************************************************************************** PP

                         TIGR00973  78 idaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvvea 154
                                       id a+ea+k+ae+ rihtf+ats++h+++kl+k+ d+v+e++v+av++a +++ +vefsaeda+r++ +fl+rv+ea
  lcl|FitnessBrowser__Miya:8501055  84 IDRAWEAVKVAENPRIHTFLATSPVHMQYKLRKEPDQVVEMAVAAVRHAAKYTSNVEFSAEDASRSNPDFLVRVFEA 160
                                       ***************************************************************************** PP

                         TIGR00973 155 aieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGe 231
                                       +i+aGattin+PdtvGya P+e+g li+++ en Pn +ka++svhch+dlG+ van+laa+k+Garq e+ti GiGe
  lcl|FitnessBrowser__Miya:8501055 161 VINAGATTINVPDTVGYAQPEEFGRLIRYVIENTPNSHKAVFSVHCHNDLGMGVANTLAALKAGARQAEVTISGIGE 237
                                       ***************************************************************************** PP

                         TIGR00973 232 raGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknkety 308
                                       raGna+lee+vmal++r+df++++ g+ t++++ t rl+s + g ++++nkaivG+nafahesGihqdG+lkn+ety
  lcl|FitnessBrowser__Miya:8501055 238 RAGNASLEEIVMALHTRRDFYQLDCGVVTEQLFPTCRLLSMIIGQPIPPNKAIVGANAFAHESGIHQDGMLKNRETY 314
                                       ***************************************************************************** PP

                         TIGR00973 309 eilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeee 385
                                       ei++pesiG +k+ lv+gk+sGr+a+k++l+elG++l+e +l  +fe+ k+ladkkk+++ded+ealvlee+ + ++
  lcl|FitnessBrowser__Miya:8501055 315 EIMTPESIGKTKTDLVIGKHSGRNAVKNKLDELGYRLEEAQLVTVFEAVKKLADKKKQIYDEDIEALVLEEVYRLPD 391
                                       ************************************************************************97776 PP

                         TIGR00973 386 eklkleklqvqsgee.svptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgev 461
                                         ++l++l+vq++++ + pta+v + v ge k+aa  G Gp+dav++ i +i++  + l+ ys+ta + g+da+gev
  lcl|FitnessBrowser__Miya:8501055 392 L-YRLVNLSVQCSDTgMPPTAAVVMDVMGEVKRAAGFGVGPIDAVFNVIGEIVGRAPVLERYSVTAITGGTDAQGEV 467
                                       6.**********9873678********************************************************** PP

                         TIGR00973 462 kvvlelngkkysGrgvatdiveasakayvnaln 494
                                       +v+l+ ng  + Grg + di+ asa+ayvnaln
  lcl|FitnessBrowser__Miya:8501055 468 TVRLRQNGSSAVGRGSDPDIILASARAYVNALN 500
                                       ********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (514 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.93
//
[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