Alignments for a candidate for hcs in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Trichormus variabilis ATCC 29413

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_011318900.1 AVA_RS10680 2-isopropylmalate synthase

Query= BRENDA::D0VY45
         (540 letters)



>NCBI__GCF_000204075.1:WP_011318900.1
          Length = 531

 Score =  465 bits (1197), Expect = e-135
 Identities = 259/524 (49%), Positives = 348/524 (66%), Gaps = 21/524 (4%)

Query: 22  PTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMI 81
           P  + I DTTLRDGEQ PGA +   +KL  A+QLA+LGVDIIEAGF  AS  DF AV  I
Sbjct: 5   PERIIIFDTTLRDGEQCPGATLNIDEKLAIAKQLARLGVDIIEAGFAFASPGDFEAVHKI 64

Query: 82  AEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRK 141
           A+ VG     NG  PVI  ++R    DI  A EA+K A + R+ TFIATS IH++YKL+K
Sbjct: 65  AQTVGT---ENG--PVICSLARARHDDIKAAAEAIKPAAKGRIHTFIATSDIHLQYKLKK 119

Query: 142 SKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTV 201
           ++ +V+  A  MV +A+S    D++F  EDA RSD EFLYQ+    I AGATT+ IPDTV
Sbjct: 120 TRPEVIAIAEEMVAYAKSF-TDDVEFSPEDAGRSDPEFLYQVLERAIAAGATTINIPDTV 178

Query: 202 GIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGI 261
           G   P E+G +I  IK N P I+ AI++ H HNDLGLA AN +E  + GARQLE TINGI
Sbjct: 179 GYTTPSEFGAIIKGIKENVPNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGI 238

Query: 262 GERAGNASFEEVVMALTCRG--IDILGGLH-------TGINTRHILKTSKMVEKYSGLHL 312
           GERAGNA+ EE+VMA+  R    +   G H       T I+T+ I KTS++V   +G+ +
Sbjct: 239 GERAGNAALEELVMAMHVRRQYFNPFLGRHPDSEEPLTNIDTKQIYKTSRLVSNLTGMLV 298

Query: 313 QPHKALVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALR 372
           QP+KA+VGANAF HESGIHQDG+LK++ TYEI+  + IGL     + IVLGK SGR A R
Sbjct: 299 QPNKAIVGANAFAHESGIHQDGVLKNKLTYEIMDAQLIGL---TDNQIVLGKHSGRNAFR 355

Query: 373 NRLEELGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVT 432
            RL+ELG++L +TE+   F +FK VA+KKK I+D DL A+V++E      ++++  +QV+
Sbjct: 356 TRLKELGFELSETELNKAFVKFKEVADKKKEISDWDLEAIVNDEIQQAPDLFRVELVQVS 415

Query: 433 CGTVGFSTATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGI 492
           CG+    TATV L + DG      +IGTGPVD+ YKAIN +V  P +L+++++ ++T GI
Sbjct: 416 CGSNARPTATVTLRTPDGEELTDAAIGTGPVDAVYKAINRVVNVPNQLIEFSVQSVTAGI 475

Query: 493 DATATTSVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536
           DA    ++ +        VFSG    TD++V+S  AY++ALN +
Sbjct: 476 DAIGEVTIRLR---YESRVFSGHAANTDIIVASAQAYVNALNRL 516


Lambda     K      H
   0.318    0.134    0.390 

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: 638
Number of extensions: 31
Number of successful extensions: 6
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: 540
Length of database: 531
Length adjustment: 35
Effective length of query: 505
Effective length of database: 496
Effective search space:   250480
Effective search space used:   250480
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: 52 (24.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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 original 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