GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Klebsiella michiganensis M5al

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BWI76_RS14455 BWI76_RS14455 aspartate aminotransferase family protein

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__Koxy:BWI76_RS14455
          Length = 447

 Score =  226 bits (577), Expect = 9e-64
 Identities = 138/425 (32%), Positives = 225/425 (52%), Gaps = 15/425 (3%)

Query: 38  IITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHP 97
           +   A+G YI D+ G + LDA  G     +G+   +++ A  RQ+  L + +  F T+  
Sbjct: 15  VAVSAQGAYITDASGQRYLDACGGAAVSCLGHAHPDVLAAMHRQIDRLAYAHTSFFTSDT 74

Query: 98  PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157
            V +LA+ +   AP  +N+ +F   GSEA +T L++ R Y+   GQP + + I R   YH
Sbjct: 75  -VEQLAEQLVRTAPGSLNYAYFVSGGSEAVETALKLARQYFVEIGQPDRTLFIARKQSYH 133

Query: 158 GSTVAGVSLGGMKALHEQGDFPIPGIVHIA--QPYWYGEGGDMSPDEFGVWAAEQLEKKI 215
           G+T+  +++GG +    Q    +  +V ++    Y   E G+ S  ++      +LE  I
Sbjct: 134 GNTLGALAVGGNEWRRRQFAPLLMDVVRVSACNEYRDREAGE-SQQQYTERLLGELEAAI 192

Query: 216 LEVGEENVAAFIAEPIQGAG-GVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEW 274
           L+ G E +  FIAE + GA  G + P   Y   +R +  KY IL+IADEV+CG GRTG  
Sbjct: 193 LDAGPEKIIGFIAETVVGATTGAMPPTPGYLQGVRRLCDKYGILYIADEVMCGMGRTGTL 252

Query: 275 FGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG-GEFYHGFTYSGHPVAAA 333
              +  G  PD++ IAKGL  GY P+G V+  ++IV  L  G G F HG TY  HP AAA
Sbjct: 253 HAFEQDGVVPDIVTIAKGLGGGYQPIGAVLASEQIVAALQAGSGMFQHGHTYICHPTAAA 312

Query: 334 VALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKKTR 393
            AL   +++  ++++E+V+ + A   Q     L   P VG+ RG G+ A +ELV +K+ +
Sbjct: 313 AALAVQQVIERDRLLEQVQQQGAYLQQALHDVLGGLPYVGDTRGRGLFAGVELVCDKERK 372

Query: 394 ERFTD-KGVGMLCREHCFRNGLIMRAV--------GDTMIISPPLVIDPSQIDELITLAR 444
             F     +    +  C  +GL++  +        GD ++I+PP ++  S++D ++    
Sbjct: 373 TAFDPLLKLHAAIKAQCMGHGLLVYPMGGTIDGQRGDHILIAPPFIVSRSELDFVVDTLH 432

Query: 445 KCLDQ 449
           K + +
Sbjct: 433 KVISE 437


Lambda     K      H
   0.320    0.138    0.425 

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: 552
Number of extensions: 34
Number of successful extensions: 5
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: 456
Length of database: 447
Length adjustment: 33
Effective length of query: 423
Effective length of database: 414
Effective search space:   175122
Effective search space used:   175122
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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