GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cimA in Synechococcus elongatus PCC 7942

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate Synpcc7942_1410 Synpcc7942_1410 2-isopropylmalate synthase

Query= curated2:O26819
         (496 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1410 Synpcc7942_1410
           2-isopropylmalate synthase
          Length = 540

 Score =  356 bits (913), Expect = e-102
 Identities = 227/524 (43%), Positives = 302/524 (57%), Gaps = 32/524 (6%)

Query: 2   QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61
           ++ + DTTLRDGEQ+PG SL  EEKL IA ++  L  DIIEAG A  S G+ E +++I +
Sbjct: 9   RILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDFEAVQRIAA 68

Query: 62  EGLRAE---ICSFARAVREDIDAAISCDVDS----VHLVVPTSDLHLEHKLRKTREEVLE 114
           E    +   ICS ARA R+DI AA      +    +H  + TSD+HLE+KL+KTR EVL 
Sbjct: 69  EVGTPDGPTICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKLKKTRAEVLA 128

Query: 115 QAVDCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERS 174
              +   YA      VE S ED+ RSD +FL       I AGA+ I   DTVG  TP   
Sbjct: 129 VIPEMVGYAASLVDDVEFSPEDAGRSDPEFLYECLEAAIAAGAKTINIPDTVGYTTPSEF 188

Query: 175 YEFYRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAA 229
                G+ +       A +SVH HND GLAVAN L  ++ GA ++  TINGIGERAGNAA
Sbjct: 189 GALIGGIKQNVCNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGIGERAGNAA 248

Query: 230 LEEVVVALK-----------SLYDVD---TSINIEMLYETSRMVARMTGVYLQPNKAIVG 275
           LEE+V+AL               D +   T +N   +Y+TSR+V+ +TG+ +QPNKAIVG
Sbjct: 249 LEELVMALHVRRQYFNPFLGRAADSEAPLTQVNTREIYKTSRLVSNLTGMLVQPNKAIVG 308

Query: 276 ENAFAHESGIHADGVLKKAETYEPITPEMVGHGRG-FVMGKHIGTHALRKRLDELGMKVA 334
            NAFAHESGIH DGVLK   TYE +  E +G       +GK  G +A R RL ELG  + 
Sbjct: 309 ANAFAHESGIHQDGVLKNKLTYEIVDAETIGLSTNRITLGKLSGRNAFRTRLQELGYDLG 368

Query: 335 DDKLMEIFRRVKTLGDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTAS 394
           +D L   F R K L D  + VTD DL+AI  D       ++  L+ V + +G+   PTA+
Sbjct: 369 EDDLNRAFLRFKELADKKREVTDRDLEAIVNDET-QQAPELFKLELVQVSAGDHARPTAT 427

Query: 395 VKLRV-DDREVLEAGTGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVI 453
           V LR  +  E+ +A  G GPVDA   AI + +       L E+ V ++T G DA+ +V I
Sbjct: 428 VTLRTPEGEELTDAAIGTGPVDAIYRAINRVVN--IPNELIEFSVKSVTAGIDAIGEVTI 485

Query: 454 KLRHGDRIISARSTQPDIIMASVEAFLSGVNRLL-ANEKSEGTH 496
           +LRH DRI S  S   DI++AS +A++  +NRL  A +K +  H
Sbjct: 486 RLRHEDRIFSGHSANTDILVASAQAYIHALNRLAEALQKDKPLH 529


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: 702
Number of extensions: 42
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: 540
Length adjustment: 35
Effective length of query: 461
Effective length of database: 505
Effective search space:   232805
Effective search space used:   232805
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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