GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Trichormus variabilis ATCC 29413

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011318900.1 AVA_RS10680 2-isopropylmalate synthase

Query= curated2:O26819
         (496 letters)



>NCBI__GCF_000204075.1:WP_011318900.1
          Length = 531

 Score =  354 bits (908), Expect = e-102
 Identities = 218/522 (41%), Positives = 308/522 (59%), Gaps = 35/522 (6%)

Query: 2   QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKI-- 59
           ++ + DTTLRDGEQ PG +L  +EKL IA ++  LG DIIEAG A  S G+ E + KI  
Sbjct: 7   RIIIFDTTLRDGEQCPGATLNIDEKLAIAKQLARLGVDIIEAGFAFASPGDFEAVHKIAQ 66

Query: 60  ---TSEGLRAEICSFARAVREDIDAAISCDVDS----VHLVVPTSDLHLEHKLRKTREEV 112
              T  G    ICS ARA  +DI AA      +    +H  + TSD+HL++KL+KTR EV
Sbjct: 67  TVGTENG--PVICSLARARHDDIKAAAEAIKPAAKGRIHTFIATSDIHLQYKLKKTRPEV 124

Query: 113 LEQAVDCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPE 172
           +  A +   YA      VE S ED+ RSD +FL  +    I AGA  I   DTVG  TP 
Sbjct: 125 IAIAEEMVAYAKSFTDDVEFSPEDAGRSDPEFLYQVLERAIAAGATTINIPDTVGYTTPS 184

Query: 173 RSYEFYRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGN 227
                 +G+ E       A +SVH HND GLAVAN L  ++ GA ++  TINGIGERAGN
Sbjct: 185 EFGAIIKGIKENVPNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGIGERAGN 244

Query: 228 AALEEVVVALK--------------SLYDVDTSINIEMLYETSRMVARMTGVYLQPNKAI 273
           AALEE+V+A+                  +  T+I+ + +Y+TSR+V+ +TG+ +QPNKAI
Sbjct: 245 AALEELVMAMHVRRQYFNPFLGRHPDSEEPLTNIDTKQIYKTSRLVSNLTGMLVQPNKAI 304

Query: 274 VGENAFAHESGIHADGVLKKAETYEPITPEMVG-HGRGFVMGKHIGTHALRKRLDELGMK 332
           VG NAFAHESGIH DGVLK   TYE +  +++G      V+GKH G +A R RL ELG +
Sbjct: 305 VGANAFAHESGIHQDGVLKNKLTYEIMDAQLIGLTDNQIVLGKHSGRNAFRTRLKELGFE 364

Query: 333 VADDKLMEIFRRVKTLGDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPT 392
           +++ +L + F + K + D  K ++D DL+AI  D +    D +  ++ V +  G+   PT
Sbjct: 365 LSETELNKAFVKFKEVADKKKEISDWDLEAIVNDEIQQAPD-LFRVELVQVSCGSNARPT 423

Query: 393 ASVKLRV-DDREVLEAGTGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDV 451
           A+V LR  D  E+ +A  G GPVDA   AI + +       L E+ V ++T G DA+ +V
Sbjct: 424 ATVTLRTPDGEELTDAAIGTGPVDAVYKAINRVVN--VPNQLIEFSVQSVTAGIDAIGEV 481

Query: 452 VIKLRHGDRIISARSTQPDIIMASVEAFLSGVNRLLANEKSE 493
            I+LR+  R+ S  +   DII+AS +A+++ +NRL A+ +++
Sbjct: 482 TIRLRYESRVFSGHAANTDIIVASAQAYVNALNRLYASLQTQ 523


Lambda     K      H
   0.317    0.135    0.373 

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: 641
Number of extensions: 37
Number of successful extensions: 8
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: 496
Length of database: 531
Length adjustment: 35
Effective length of query: 461
Effective length of database: 496
Effective search space:   228656
Effective search space used:   228656
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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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:

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:

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:

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:

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