GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__ANA3:7024902 Shewana3_2076 inner membrane ABC
           transporter permease protein YjfF (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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