Alignments for a candidate for cimA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Synechococcus elongatus PCC 7942

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate Synpcc7942_1410 Synpcc7942_1410 2-isopropylmalate synthase

Query= curated2:O26819
         (496 letters)



>FitnessBrowser__SynE:Synpcc7942_1410
          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 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