GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjtF in Skermanella stibiiresistens SB22

Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate WP_037452166.1 N825_RS13095 ribose ABC transporter permease

Query= SwissProt::P37772
         (331 letters)



>NCBI__GCF_000576635.1:WP_037452166.1
          Length = 338

 Score =  154 bits (388), Expect = 4e-42
 Identities = 110/315 (34%), Positives = 172/315 (54%), Gaps = 18/315 (5%)

Query: 3   KRNLPLMI-TIGVFVLGYLYCLT-QFPG--FASTRVICNILTDNAFLGIIAVGMTFVILS 58
           K+NL  +I  +G+  +  L C+  +F    F + R I  ++   +   ++A G+TFVIL+
Sbjct: 25  KQNLHTIIQVVGMLPVLILICIGFEFATGKFLTARNISIVMQQASINIVLATGLTFVILT 84

Query: 59  GGIDLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFI 118
           GGIDL+VG+V+A + V    +       P LA PL L++G A GA  G LI   ++P FI
Sbjct: 85  GGIDLAVGAVLAVSAVTAVSMT--LTGMPDLAIPLALLVGLALGAVNGSLIAFFRLPPFI 142

Query: 119 ITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSA---MGLLMLAVVVI 175
           +TL  M  +RG+S L + ++      +++     AW   G  +L     M ++ LAVV I
Sbjct: 143 VTLGAMTAVRGLSRLSANDTT-----VFNAALPFAWI--GNSQLFGIPWMVIIALAVVAI 195

Query: 176 GIFLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYT-QA 234
             F+  RT  G  +Y +GGN  +A L GI   +  + +Y +S  LA LAG++ +  T  A
Sbjct: 196 SWFVLRRTVLGVWIYGVGGNPDAARLSGIKVWAVLLFVYAISGMLAGLAGVMSAARTLSA 255

Query: 235 GYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTK 294
             A  G+G ELDAIA+V++GGT   GG+G++ GTL G  I  ++   +     +S  W  
Sbjct: 256 NGAQLGMGYELDAIAAVILGGTSFVGGIGSIFGTLIGALIIAVLSNGLIL-MNVSEVWQL 314

Query: 295 IAIGILLFIFIALQR 309
           I  G+++   +AL R
Sbjct: 315 IIKGLVIVGAVALDR 329


Lambda     K      H
   0.329    0.145    0.428 

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: 295
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: 331
Length of database: 338
Length adjustment: 28
Effective length of query: 303
Effective length of database: 310
Effective search space:    93930
Effective search space used:    93930
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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