GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01112 in Shewanella sp. ANA-3

Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 7024902 Shewana3_2076 inner membrane ABC transporter permease protein YjfF (RefSeq)

Query= reanno::Burk376:H281DRAFT_01112
         (364 letters)



>FitnessBrowser__ANA3:7024902
          Length = 320

 Score =  132 bits (331), Expect = 2e-35
 Identities = 100/322 (31%), Positives = 163/322 (50%), Gaps = 39/322 (12%)

Query: 50  PEWFTVALIVVTCLIVGAINPRFFQFAT---LFDLLHSATTMSLFALGTLVVLASGGIDV 106
           P W T +L++ T  +VG    +F  FA+   + +LL     + + ALG  +V+ SGGID+
Sbjct: 8   PLWITASLLL-TMFLVGTF--QFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDL 64

Query: 107 SFTAIAALTMYGITKAV----FAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSL 162
           S  A+ AL+  G+  ++    + W P   F +IL  G L G ++G +    +H  K    
Sbjct: 65  SVGAVIALS--GVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTI----IHVYKLQPF 118

Query: 163 IVTIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLP------VS 216
           IVT+   +L RGL  T    +  ++ P            FY     +   LP      +S
Sbjct: 119 IVTLAGMFLARGLATTLSEESIAIDHP------------FYDAVAEMSIALPGNGALDLS 166

Query: 217 VLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAG 276
            L  +   V+   +++ T  G  VYA+GG+   AE +G ++    + ++  +  LA +AG
Sbjct: 167 SLIFILFFVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAG 226

Query: 277 ILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILV 336
           I+             +G ELD IAAV++GG  +TGG+G V+GT+LGV+L+ +I++ +   
Sbjct: 227 IVFTFYTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFD 286

Query: 337 G-VPSTWQKVIIGA----FILL 353
           G + S W K++IG     FILL
Sbjct: 287 GSLSSWWTKIVIGLLLFFFILL 308


Lambda     K      H
   0.328    0.141    0.426 

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: 310
Number of extensions: 19
Number of successful extensions: 4
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: 364
Length of database: 320
Length adjustment: 29
Effective length of query: 335
Effective length of database: 291
Effective search space:    97485
Effective search space used:    97485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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