GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Shewanella sp. ANA-3

Align Ribose import permease protein RbsC (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= SwissProt::P0AGI1
         (321 letters)



>FitnessBrowser__ANA3:7024902
          Length = 320

 Score =  158 bits (400), Expect = 1e-43
 Identities = 105/315 (33%), Positives = 174/315 (55%), Gaps = 18/315 (5%)

Query: 10  RYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLF-NILQQTSVNAIMAVGMTLVIL 68
           R F   W+       +LL+ + +V T   + F    +  N+L+  +   I A+GMTLVI+
Sbjct: 4   RRFIPLWITA-----SLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVII 58

Query: 69  TSGIDLSVGSLLALTGAVAASIVG-IEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAF 127
           + GIDLSVG+++AL+G V + ++   + + L+A    L LG   GA+ G I+   ++Q F
Sbjct: 59  SGGIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPF 118

Query: 128 IATLVMMLLLRGVTMVYTNGS-PVNTGFTENADLFGWFGIGRP----LGVPTPVWIMGIV 182
           I TL  M L RG+    +  S  ++  F    D      I  P    L + + ++I+  V
Sbjct: 119 IVTLAGMFLARGLATTLSEESIAIDHPFY---DAVAEMSIALPGNGALDLSSLIFILFFV 175

Query: 183 FLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARL 242
            +A   ++H+TR G  +YA+GGN+ +  L GI++ K  I +Y++   LA+LAGI+     
Sbjct: 176 IIAV--VMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYT 233

Query: 243 SSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLG-VSSYY 301
            S       G ELDAIAAVV+GGT L GG G ++GT++G +++G +   +   G +SS++
Sbjct: 234 FSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWW 293

Query: 302 QMIVKAVVILLAVLV 316
             IV  +++   +L+
Sbjct: 294 TKIVIGLLLFFFILL 308


Lambda     K      H
   0.324    0.139    0.393 

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: 266
Number of extensions: 12
Number of successful extensions: 2
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: 321
Length of database: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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