GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Shewanella loihica PV-4

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 5210162 Shew_2606 ABC transporter-related protein (RefSeq)

Query= uniprot:D8IUY7
         (241 letters)



>FitnessBrowser__PV4:5210162
          Length = 272

 Score =  220 bits (561), Expect = 2e-62
 Identities = 122/244 (50%), Positives = 169/244 (69%), Gaps = 7/244 (2%)

Query: 3   TNILKVQQLSVAYGG-IQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVE 61
           T +L +  + V Y   IQ ++G+ +EV +GE+VTL+G NGAGK+TTLKAI+G L     E
Sbjct: 11  TPLLAINNIEVVYDDVIQVLRGVSIEVPQGEIVTLLGPNGAGKSTTLKAISGLLKTENGE 70

Query: 62  ---GHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAA 118
              G I ++G+ +  K + ++V+  L  V EGR +   M++ ENL +GAYT  D GQ+  
Sbjct: 71  VSRGDIHFMGERIDVKNADDVVRSGLFQVMEGRRIVEDMTVIENLKLGAYTRRD-GQVNQ 129

Query: 119 DIDKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEK 178
           DI+  F  FPRLKER   +AG LSGGEQQMLA+ RALM+ PK++ LDEPSMGLSP++V++
Sbjct: 130 DIEMVFNYFPRLKERTG-LAGYLSGGEQQMLAIGRALMARPKMICLDEPSMGLSPLLVKE 188

Query: 179 IFEVIRNVS-AQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAY 237
           +F +I  ++  QGIT+LLVEQNA  AL+AA+ GY+MESG I + G   Q+L++  VK  Y
Sbjct: 189 VFGIIEKINREQGITMLLVEQNANYALKAANYGYIMESGKIVLDGTKAQLLNNEDVKEFY 248

Query: 238 LGEG 241
           LG G
Sbjct: 249 LGGG 252


Lambda     K      H
   0.317    0.134    0.365 

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: 206
Number of extensions: 9
Number of successful extensions: 5
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: 241
Length of database: 272
Length adjustment: 24
Effective length of query: 217
Effective length of database: 248
Effective search space:    53816
Effective search space used:    53816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 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