GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Shewanella loihica PV-4

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 5210055 Shew_2502 ABC transporter-related protein (RefSeq)

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__PV4:5210055
          Length = 261

 Score =  108 bits (269), Expect = 2e-28
 Identities = 79/264 (29%), Positives = 139/264 (52%), Gaps = 20/264 (7%)

Query: 1   MKEILLKAENVR-----AYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVI 55
           MK  LLK   +       Y   ++    A++ +SFE+   E + +VGE+G GK+TL+ ++
Sbjct: 1   MKSPLLKVNRLSKTFFAGYKGFKRQYNHALEPISFELNRGETLAIVGETGSGKSTLARIL 60

Query: 56  FMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM 115
               V      DG+I     GE +E  ++       K   + I +I Q    +L P + +
Sbjct: 61  ----VGAEQRTDGEILFE--GEALESRNL-------KQRCRLIRMIFQDPNTSLNPRLTV 107

Query: 116 EKYVRH-LAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174
            + +   L  +  +D++    +      +VGL P     YP  +S GM+QR  +A A +L
Sbjct: 108 GELLDEPLRFNTDLDKQARFAQVVDTLRKVGLLPEHADFYPHMISEGMKQRVAVARALML 167

Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234
           NP ++IADE  +ALD+  +  +L +L+++ +Q +  S IF++H++  +R  +D++++++ 
Sbjct: 168 NPKIIIADEALTALDLSVRSQILNLLLKL-QQEMGLSYIFVSHNMNIIRHFSDKIMVLHQ 226

Query: 235 GKIVEFAPVESLLEKPLHPYTQGL 258
           GK+VE A  E L   P H YTQ L
Sbjct: 227 GKMVEKATTEKLFNAPEHEYTQRL 250


Lambda     K      H
   0.321    0.138    0.405 

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: 204
Number of extensions: 10
Number of successful extensions: 3
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: 330
Length of database: 261
Length adjustment: 26
Effective length of query: 304
Effective length of database: 235
Effective search space:    71440
Effective search space used:    71440
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: 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