GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Flavobacterium glycines Gm-149

Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_066325976.1 BLR17_RS13745 2-isopropylmalate synthase

Query= curated2:Q8TYM1
         (509 letters)



>NCBI__GCF_900100165.1:WP_066325976.1
          Length = 391

 Score =  281 bits (719), Expect = 3e-80
 Identities = 156/375 (41%), Positives = 227/375 (60%), Gaps = 9/375 (2%)

Query: 12  DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71
           D+V+IFDTTLRDGEQ PG  L   +KL IA +LD +GVD IEAGF  +S G+  ++  I+
Sbjct: 4   DKVQIFDTTLRDGEQVPGCKLDTNQKLVIAERLDNMGVDIIEAGFPVSSPGDFLSVTEIS 63

Query: 72  REELDAEVCSMARMVKGDVDAAV----EAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127
           +   +A VC + R VK D+D A      A+   +H  + TSE H+  KL+  RE+++ RA
Sbjct: 64  KIVKNATVCGLTRAVKNDIDVAAAALKHAKRPRIHTGIGTSESHILHKLQTTREDIIARA 123

Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187
           +  V +A+ +   VE   ED  RT+  +L +V +  +++GA  L   DT G   PE    
Sbjct: 124 KAAVAHAKSYVEDVEFYAEDAGRTDNAFLAQVCEEVIKSGATVLNIPDTTGYCLPEEYGA 183

Query: 188 AVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245
            +K L+E V   E+V +S HCH+D GMATAN+++    GARQ+  T+NGIGERAGN ALE
Sbjct: 184 KIKYLKENVKGIENVTISCHCHNDLGMATANSISGAINGARQIECTINGIGERAGNTALE 243

Query: 246 EVVVVLEELYGVD--TGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303
           EVV++ ++   ++  T I T++L E+S+LV    G+ V PNKA+VG NAF H SGIH DG
Sbjct: 244 EVVMIFKQHPDLNLYTDIDTKQLNEMSRLVSESMGMMVQPNKAIVGANAFAHSSGIHQDG 303

Query: 304 ILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362
           ++K+ +TYE I P  VG +E   VL    G + +  + K++G ++   QL  +     + 
Sbjct: 304 VIKNRATYEIIDPLDVGVNESSIVLTARSGRAALAYRAKKVGYELTKNQLDVVYVEFLKF 363

Query: 363 GDRGKRITEADLRAI 377
            D  K I + D+  I
Sbjct: 364 ADVKKEILDDDIHLI 378


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: 491
Number of extensions: 32
Number of successful extensions: 4
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: 391
Length adjustment: 32
Effective length of query: 477
Effective length of database: 359
Effective search space:   171243
Effective search space used:   171243
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: 51 (24.3 bits)

This GapMind analysis is from Jul 26 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