GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Shewanella loihica PV-4

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__PV4:5207560
          Length = 369

 Score =  145 bits (366), Expect = 2e-39
 Identities = 84/213 (39%), Positives = 126/213 (59%), Gaps = 8/213 (3%)

Query: 30  GEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVND------LPARERNVAMVFQ 83
           GE + ++GPSG GKST++RMIAGL     G +R G +V         L  ++R++  V Q
Sbjct: 29  GEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQRHLGYVPQ 88

Query: 84  NYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQQQRA 143
           ++ L+P+M+   N+   L  +  P AE   R ++    +NL  L +R P  +SGGQ+QR 
Sbjct: 89  HFGLFPNMTALANVVAALDHI--PKAERVARAKDWLERVNLHGLPDRLPANLSGGQRQRV 146

Query: 144 AIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTLAD 203
           A+ARA+ + P V L DEP S +D + R +L  ++ RL ++L    + VTHD  EA+ LAD
Sbjct: 147 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIMVTHDLNEALLLAD 206

Query: 204 RVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG 236
           R+IL+  G ++Q GSP E+   PRN   A  +G
Sbjct: 207 RMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239


Lambda     K      H
   0.321    0.137    0.403 

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: 311
Number of extensions: 7
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: 406
Length of database: 369
Length adjustment: 30
Effective length of query: 376
Effective length of database: 339
Effective search space:   127464
Effective search space used:   127464
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: 50 (23.9 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