GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Azoarcus olearius BH72

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011766887.1 AZO_RS15865 2-isopropylmalate synthase

Query= curated2:Q8TYM1
         (509 letters)



>NCBI__GCF_000061505.1:WP_011766887.1
          Length = 511

 Score =  380 bits (976), Expect = e-110
 Identities = 216/505 (42%), Positives = 316/505 (62%), Gaps = 20/505 (3%)

Query: 12  DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71
           D + IFDTTLRDGEQ+PG ++T +EKLRIAR+L+ + VD IEAGFAAAS G+ +++R IA
Sbjct: 3   DALIIFDTTLRDGEQSPGASMTRDEKLRIARQLERMRVDVIEAGFAAASNGDFESVRSIA 62

Query: 72  REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127
               ++ VCS+AR  + D+  A EA   A    +H  + TS +H++KKLRM  ++V+E+A
Sbjct: 63  EAIKESTVCSLARANENDIRRAGEAIRPAARGRIHTFIATSPIHMEKKLRMTPDQVVEQA 122

Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187
            + + +AR++   +E S ED  R+E+++L  +FDA ++AGA+ +   DTVG   PE    
Sbjct: 123 VKAIGWAREYTDDIEFSAEDAGRSEIDFLCRIFDAVIKAGAKTINVPDTVGYNVPEQYAA 182

Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245
            ++ L ERV   + VI SVHCH+D G+A +N++AAV AGARQV  T+NG+GERAGNA+LE
Sbjct: 183 TLRTLIERVPNADKVIWSVHCHNDLGLAVSNSLAAVMAGARQVECTINGLGERAGNASLE 242

Query: 246 EVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302
           E+V+ +    +++ V T I T ++   SKLV ++TG  V PNKA+VG NAF HESGIH D
Sbjct: 243 EIVMAVRTRADVFPVSTNIDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHESGIHQD 302

Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDV-DDEQLLEILRRLK 360
           G+LK   TYE +  E VG    + VLGKH G +  R +L+++G+++  +EQL     R K
Sbjct: 303 GVLKHRETYEIMRAEDVGWGANKLVLGKHSGRNAFRARLQELGIEIGSEEQLNHAFARFK 362

Query: 361 RLGDRGKRITEADLRAIAEDVLGRPAERDIEV--EDFTTVTGKRTIPTASIVVKIDGTRK 418
            L D+   I + DL A+  D    P +    +    F + TG+   P A + + I G   
Sbjct: 363 ELADKKHEIFDEDLHALMSDEAVTPEQEHFRLVATRFHSETGE--TPRAEVTLAIGGQET 420

Query: 419 EAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDI 478
            + + G GPVDA  KA+E      G   EL+ Y   A+T GTDA   V V+L   + G +
Sbjct: 421 RSQAEGSGPVDAAFKAIESV---AGSGSELLLYSVNAITTGTDAQGEVTVRL--AKDGRV 475

Query: 479 VHSGSSREDIVVASLEAFIDGINSL 503
           V+   +  DI+VAS +A+++ +N L
Sbjct: 476 VNGQGADTDIIVASAKAYLNALNKL 500


Lambda     K      H
   0.315    0.134    0.367 

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: 628
Number of extensions: 32
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: 509
Length of database: 511
Length adjustment: 34
Effective length of query: 475
Effective length of database: 477
Effective search space:   226575
Effective search space used:   226575
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 (21.6 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