GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamD in Pedobacter sp. GW460-11-11-14-LB5

Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate CA265_RS02450 CA265_RS02450 hypothetical protein

Query= uniprot:Q39TW0
         (387 letters)



>FitnessBrowser__Pedo557:CA265_RS02450
          Length = 262

 Score =  184 bits (467), Expect = 2e-51
 Identities = 98/242 (40%), Positives = 148/242 (61%), Gaps = 7/242 (2%)

Query: 146 EGMELLYFTGCYLSYDPRMRKVAAATAAILNKAGVDFGILGSKESCCGESIRKTGNEELF 205
           E  E+L++ GC  SYD R +K+      IL+  G+ + +LG++ESC G+  ++ GNE LF
Sbjct: 16  EEPEILFWVGCAGSYDERAQKITRDICKILHHVGIKYAVLGTEESCTGDPAKRAGNEFLF 75

Query: 206 KRLAKENIKQFIDNGVTKILVSSPHCYHTFVNEYPEFKVNFEVVFISQYIGQLINEGRLQ 265
           +  A  NI+      + KI+   PHC++T  NEYP     +EV+  +Q I  LINEG+L+
Sbjct: 76  QMQAMTNIEVLNAYNIKKIVTGCPHCFNTIKNEYPGLGGTYEVIHHTQLIQDLINEGKLK 135

Query: 266 ITGEFA---KKVTYHDPCYLGRHNGIYDEPRQVLQQVPGLELLEMADNRESSLCCGGGGG 322
             G  +   KK+TYHDPCYLGR NGIY+ PR+ L +V   +L+EM   + + LCCG GG 
Sbjct: 136 AEGGESFKGKKITYHDPCYLGRGNGIYEAPRKAL-EVLDAQLVEMKRCKSNGLCCGAGGA 194

Query: 323 RIWMETPKEERFADL-RIRQAVDVGATVLATSCPYCITNFTDSSLDLADHE-KVEVKDLA 380
           +++ E  K  +  ++ RI +A+     V+A  CP+C+T  +D  + L D E +V+V D+A
Sbjct: 195 QMFKEPEKGNKDINVERIDEALQTNPQVIAAGCPFCMTMLSD-GIKLKDKEQEVKVLDIA 253

Query: 381 EI 382
           EI
Sbjct: 254 EI 255


Lambda     K      H
   0.320    0.139    0.427 

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: 323
Number of extensions: 19
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: 387
Length of database: 262
Length adjustment: 27
Effective length of query: 360
Effective length of database: 235
Effective search space:    84600
Effective search space used:    84600
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: 48 (23.1 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