GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cimA in Acidovorax sp. GW101-3H11

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate Ac3H11_530 2-isopropylmalate synthase (EC 2.3.3.13)

Query= curated2:Q8TYM1
         (509 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_530 2-isopropylmalate
           synthase (EC 2.3.3.13)
          Length = 512

 Score =  360 bits (925), Expect = e-104
 Identities = 210/512 (41%), Positives = 315/512 (61%), Gaps = 27/512 (5%)

Query: 12  DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71
           D++ IFDTTLRDGEQ+PG ++T +EKLRIAR+L+ + VD IEAGFAA+S G+ +A++ IA
Sbjct: 3   DKLIIFDTTLRDGEQSPGASMTKDEKLRIARQLERLKVDVIEAGFAASSNGDFEAVQAIA 62

Query: 72  REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127
               D+ +CS++R    D+  A EA   A    +H  + TS +H++KKLRM  E+VLE+A
Sbjct: 63  NAIKDSTICSLSRANDRDISRAAEALRGANSARIHTFIATSALHMEKKLRMTPEQVLEQA 122

Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187
           ++ V +AR+    +E S EDG R++ ++L  V +A +  GA  +   DTVG   PE    
Sbjct: 123 KQSVRFARNLVADIEFSPEDGYRSDPDFLCRVLEAVITEGATTINVPDTVGYAVPELYGN 182

Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVR-AGARQVHVTVNGIGERAGNAAL 244
            +K LRER+   +  I SVHCH+D GMA AN++A V+  GARQV  T+NG+GERAGN +L
Sbjct: 183 FIKTLRERIPNSDKAIWSVHCHNDLGMAVANSLAGVKIGGARQVECTINGLGERAGNCSL 242

Query: 245 EEVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHA 301
           EE+V+ +   ++ +G+D  I T+ +   S++V + TG  V PNKAVVG NAF H SGIH 
Sbjct: 243 EEIVMAVKTRKDYFGLDLAIDTQHIVAASRMVSQTTGFVVQPNKAVVGANAFAHASGIHQ 302

Query: 302 DGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEI-LRRL 359
           DG+LK   TYE +  E VG    + VLGK  G +  +++L+++GV +D E  + +   + 
Sbjct: 303 DGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGVQLDSETEINVAFAKF 362

Query: 360 KRLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTV-----TGKRTIPTASIVVKID 414
           K L DR   I + D+ A+  D        + E   F ++     TG++  P A IV  +D
Sbjct: 363 KELADRKSEIFDEDILALVSD---ESVTAEKEQYGFVSLFQQSETGEQ--PRARIVFTVD 417

Query: 415 GTRKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPE 474
           G      S G GPVDA++KA+E  +K      E+V Y   A++G T++   V V+L++  
Sbjct: 418 GQEVRGESDGNGPVDASLKAIESHVKSGA---EMVLYSVNAISGSTESQGEVTVRLQN-- 472

Query: 475 TGDIVHSGSSREDIVVASLEAFIDGINSLMAR 506
           +G +V+   +  DIVVAS +A++  +N L ++
Sbjct: 473 SGRVVNGVGADPDIVVASAKAYLSALNKLQSK 504


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: 585
Number of extensions: 23
Number of successful extensions: 9
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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