GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proC in Klebsiella michiganensis M5al

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate BWI76_RS14970 BWI76_RS14970 pyrroline-5-carboxylate reductase

Query= curated2:P74572
         (267 letters)



>FitnessBrowser__Koxy:BWI76_RS14970
          Length = 262

 Score =  137 bits (344), Expect = 3e-37
 Identities = 89/270 (32%), Positives = 146/270 (54%), Gaps = 16/270 (5%)

Query: 4   QLGIIGGGVMAEAILARLIAEKTYAPEEIIVGEPHGARRDYLQKTYQVRVSPDNQEAANV 63
           ++  IG G MAEAI+   ++      + I + +   AR ++L   Y  R+S D     N 
Sbjct: 3   KIHFIGAGQMAEAIIRASLSNGALRADAISLEDIDSARAEHLYAHY--RLSGDG--GVNE 58

Query: 64  SEVLLLAVKPQ-----VLDRVLASLAGGANRPLVISILAGVSLQRIQKGFPDHA-IIRAM 117
           + +L+L ++PQ     V +RV A L G      V+S++AGV+L+++   F +   I RA+
Sbjct: 59  ASLLVLGIRPQDDLAGVANRVRAQLNGLTT---VVSLIAGVTLEKLASLFGEATPIARAI 115

Query: 118 PNTPATVGAGMTAIAANKMVEPDQLAKAKAIFSAVGNVVEVPENLMDAVTGVSGSGPAYV 177
           PNT    G G + +  N        A+ +      G V+ +PE L+D  TG + +GP Y+
Sbjct: 116 PNTLTDTGFGYSGVTLNAHASA---AEIEPFLRGFGKVLYLPERLIDIFTGFAVAGPNYI 172

Query: 178 ALMIEALADGGVLAGLPRAIAQKLALQTVLGTAELIKETEEHPAQIKDKVTSPGGTTIAG 237
              IE+  D GVLAGL R  A ++ L+ +LG  E+++++++HP Q+ D   SP G  I G
Sbjct: 173 YYFIESFTDAGVLAGLSRPQATEVVLENLLGAVEMLRQSQKHPRQLLDINNSPAGVGIHG 232

Query: 238 VAVLEKMGFRSAIIEAVRAAYRRSQELGKK 267
           +  L    F + +  +V AA RR++ELG++
Sbjct: 233 LYELNNSDFAAGLQRSVLAAVRRTRELGQR 262


Lambda     K      H
   0.316    0.133    0.358 

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: 210
Number of extensions: 12
Number of successful extensions: 3
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: 267
Length of database: 262
Length adjustment: 25
Effective length of query: 242
Effective length of database: 237
Effective search space:    57354
Effective search space used:    57354
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: 47 (22.7 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