GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Cupriavidus basilensis 4G11

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate RR42_RS05465 RR42_RS05465 2-isopropylmalate synthase

Query= curated2:Q8TYM1
         (509 letters)



>FitnessBrowser__Cup4G11:RR42_RS05465
          Length = 512

 Score =  360 bits (923), Expect = e-104
 Identities = 213/506 (42%), Positives = 310/506 (61%), Gaps = 22/506 (4%)

Query: 12  DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71
           D++ IFDTTLRDGEQ+PG ++T EEK+RIAR+L+ + VD IEAGFAA+S G+ +AIR IA
Sbjct: 3   DKLIIFDTTLRDGEQSPGASMTREEKIRIARQLERLKVDVIEAGFAASSNGDFEAIRSIA 62

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

Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187
            + V +AR     +E S EDG+R+++++L  V +  ++ GA  +   DTVG   PEG   
Sbjct: 123 IQAVRFARQFTDDIEFSPEDGSRSDMDFLCRVLEGVIKEGATTINLPDTVGYAVPEGYAG 182

Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVR-AGARQVHVTVNGIGERAGNAAL 244
            ++ +RER+   +  I SVHCH+D GMA AN++AAV+  GARQV  T+NG+GERAGN +L
Sbjct: 183 LIRSVRERIPNSDKAIWSVHCHNDLGMAVANSLAAVKLGGARQVECTINGLGERAGNTSL 242

Query: 245 EEVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHA 301
           EEVV+ ++   + + +D G+ T ++   SKLV ++TG  V PNKAVVG NAF H SGIH 
Sbjct: 243 EEVVMAVKTRRDYFDMDVGVDTTQIVPASKLVSQITGFVVQPNKAVVGANAFAHASGIHQ 302

Query: 302 DGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDE-QLLEILRRL 359
           DG+LK   TYE +  E VG    + VLGK  G +  +++L+++G++++ E ++     R 
Sbjct: 303 DGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIELESEGEVNAAFTRF 362

Query: 360 KRLGDRGKRITEADLRAIAEDVLGRPAE--RDIEVEDFTTVTGKRTIPTASIVVKIDGTR 417
           K L D+   I + D+ AI  D      E  R I +   +  TG+R  P A +V  +DG  
Sbjct: 363 KELADQKSEIFDEDIMAIVSDEAHDVNEHFRFISLSQHSE-TGER--PHARVVFNMDGNE 419

Query: 418 KEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGD 477
                 G GPVDAT+ A+E  +       ELV Y   A+T GT A   V V+L   + G 
Sbjct: 420 VTGEGEGNGPVDATLHAIEGKVASGA---ELVLYSVNAITAGTQAQGEVTVRL--SKGGR 474

Query: 478 IVHSGSSREDIVVASLEAFIDGINSL 503
           IV+   +  DIV AS +A++  +N L
Sbjct: 475 IVNGVGTDPDIVAASAKAYLAALNKL 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: 630
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: 512
Length adjustment: 35
Effective length of query: 474
Effective length of database: 477
Effective search space:   226098
Effective search space used:   226098
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 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 (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