Alignments for a candidate for cimA in Methylohalobius crimeensis 10Ki

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Methylohalobius crimeensis 10Ki

Align (R)-citramalate synthase CimA; LiCMS; EC 2.3.3.21 (characterized)
to candidate WP_321162844.1 H035_RS0104410 alpha-isopropylmalate synthase regulatory domain-containing protein

Query= SwissProt::Q8F3Q1
         (516 letters)



>NCBI__GCF_000421465.1:WP_321162844.1
          Length = 520

 Score =  492 bits (1266), Expect = e-143
 Identities = 248/515 (48%), Positives = 348/515 (67%), Gaps = 5/515 (0%)

Query: 1   MTKVETRLEILDVTLRDGEQTRGVSFSTSEKLNIAKFLLQKLNVDRVEIASARVSKGELE 60
           M     R+EI+D TLRDGEQT+GVSFS  EK++IAK LL+++ VDR+EIASARVS  E E
Sbjct: 9   MNNPSRRIEIMDTTLRDGEQTQGVSFSPEEKISIAKALLERVRVDRIEIASARVSDREKE 68

Query: 61  TVQKIMEWAATEQLTERIEILGFVDGNKTVDWIKDSGAKVLNLLTKGSLHHLEKQLGKTP 120
            V +I  W      ++R+E+LGFVD  ++VDWI ++G   +NLLTKGS  H   QLGK  
Sbjct: 69  AVTQINAWTREAGFSDRVEVLGFVDHTRSVDWIMETGGGTINLLTKGSEKHCRTQLGKNL 128

Query: 121 KEFFTDVSFVIEYAIKSGLKINVYLEDWSNGFRNSPDYVKSLVEHLSKEHIERIFLPDTL 180
           +    D+   + YA   GL +NVYLEDWSNG+R+SP YV +L+++L    I+R  LPDTL
Sbjct: 129 ETHTQDILETVAYAHTKGLIVNVYLEDWSNGYRDSPQYVFALMDNLRGAGIQRFMLPDTL 188

Query: 181 GVLSPEETFQGVDSLIQKYPDIHFEFHGHNDYDLSVANSLQAIRAGVKGLHASINGLGER 240
           GV++PEE +  +  +  +YP++HFEFH HNDY L+ AN + A++AG  G+H ++N LGER
Sbjct: 189 GVMTPEEVYASIHDMCVRYPELHFEFHPHNDYGLATANVMAAVQAGAAGVHCTVNCLGER 248

Query: 241 AGNTPLEALVTTIHDKSNSKTNINEIAITEASRLVEVFSGKRISANRPIVGEDVFTQTAG 300
           AGN  L  +V T+ DK   +  +NE  +   S +VE FSGKR+SAN PIVG DVFTQTAG
Sbjct: 249 AGNASLAEVVVTLKDKLGVELTVNESQLVRISDMVERFSGKRVSANAPIVGADVFTQTAG 308

Query: 301 VHADGDKKGNLYANPILPERFGRKRSYALGKLAGKASISENVKQLGMVLSEVVLQKVLER 360
           +HADGD KGNLY + + PERF R RSYALGK++GKAS+ +N+++LG+ L+    + VL+R
Sbjct: 309 IHADGDHKGNLYQSRLKPERFSRVRSYALGKMSGKASLRKNLERLGIELTAEQERHVLKR 368

Query: 361 VIELGDQNKLVTPEDLPFIIADVSGRTGEKVLTIKSCNIHSGIGIRPHAQIELEYQGKIH 420
           ++ LGD  + +T +DLPFIIADV      + + + +  I SG+ +   A I +  +G+ H
Sbjct: 369 IVSLGDSKQTITTDDLPFIIADVLESESYQHIRLLNYAITSGLDLESTASIRVAVRGEAH 428

Query: 421 KEISEGDGGYDAFMNALTKITNRLGISIPKLIDYEVRIPPGGKTDALVETRITWNKSLDL 480
               +G+GG+DAF++AL ++      ++P L+DYEVRIP GG T+AL E  I+W+     
Sbjct: 429 TAAGKGNGGFDAFIDALNQVMAHYDYTLPPLLDYEVRIPKGGHTNALTECIISWDC---- 484

Query: 481 EEDQTFKTMGVHPDQTVAAVHATEKMLNQILQPWQ 515
            E +T  T GVH +Q  A++ AT K++N  L+  Q
Sbjct: 485 -EHRTRVTRGVHVNQVFASMLATLKLINIELEERQ 518


Lambda     K      H
   0.315    0.134    0.379 

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: 759
Number of extensions: 21
Number of successful extensions: 1
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: 516
Length of database: 520
Length adjustment: 35
Effective length of query: 481
Effective length of database: 485
Effective search space:   233285
Effective search space used:   233285
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 (21.5 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