GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Azospirillum brasilense Sp245

Align Uncharacterized protein (characterized, see rationale)
to candidate AZOBR_RS25115 AZOBR_RS25115 Fe-S oxidoreductase

Query= uniprot:E4PLR5
         (279 letters)



>FitnessBrowser__azobra:AZOBR_RS25115
          Length = 256

 Score =  268 bits (685), Expect = 9e-77
 Identities = 136/246 (55%), Positives = 173/246 (70%), Gaps = 2/246 (0%)

Query: 27  EKPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEAKA 86
           E+PE+V  FGTC+VDLF+PEAG+  + LL+ +GVRV FPQ QSCCGQPA+ SGYR+EA  
Sbjct: 13  ERPESVYFFGTCLVDLFYPEAGMAGMELLKAQGVRVVFPQGQSCCGQPAYNSGYREEALK 72

Query: 87  VARAQLDILDRSGLPVVVPSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEFLL 146
           VARAQLD       P+VVPSGSCAGM   H+P LF  EPD   R   +A R +ELT+FL+
Sbjct: 73  VARAQLDYFP-GDWPIVVPSGSCAGMMSKHWPDLFKGEPDEA-RARQVASRVWELTQFLV 130

Query: 147 KVCRVQLADRGAPSKIALHTSCSARREMNTHLHARELLQQLEGVERIDHDHESECCGFGG 206
           +V +V+  D+G P KI  H SC A+REM      + LL+QL  VE ++   E ECCGFGG
Sbjct: 131 QVLKVKFEDQGPPVKITWHASCHAQREMGVTDEPKALLRQLANVELVELQREKECCGFGG 190

Query: 207 TFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRGRHLASFL 266
           TF+VR PE+S AMV DK   + ++GA  +V+ D GCLMNI+G+LE  K+  RG H+A FL
Sbjct: 191 TFAVRHPEISAAMVGDKVADIENTGAKAVVSGDCGCLMNISGALEGGKKPVRGVHIAQFL 250

Query: 267 WERTNG 272
            ERT+G
Sbjct: 251 KERTHG 256


Lambda     K      H
   0.320    0.134    0.406 

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: 280
Number of extensions: 7
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: 279
Length of database: 256
Length adjustment: 25
Effective length of query: 254
Effective length of database: 231
Effective search space:    58674
Effective search space used:    58674
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: 47 (22.7 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