GapMind for catabolism of small carbon sources

 

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

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  196 bits (498), Expect = 8e-55
 Identities = 115/283 (40%), Positives = 174/283 (61%), Gaps = 22/283 (7%)

Query: 17  TAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFV 76
           T +R + L +  GE   LLGPSGCGKTT L+ IAGL+  S+G+I I  +L++ PE   FV
Sbjct: 17  TILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRLLSGPET--FV 74

Query: 77  PPKDRDIAMVFQSYALYPHMTVYDNIAFPLK-LRKVPRQEIDQRVREVAELLGLTELLNR 135
           P + R++ M+FQ YAL+PH+TV +NI F +K L K  RQ    R+ E+  L+ L  L  R
Sbjct: 75  PSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQA---RLGEMLALVKLEGLGGR 131

Query: 136 KPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIY 195
            P ELSGGQ+QRV++ RA+  +P++ L+DEP SN+DAK+R  M  E++++ +Q GV+ ++
Sbjct: 132 YPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEIREILKQRGVSAVF 191

Query: 196 VTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPPMNFLDAIVTED 255
           VTH + EA    D++A+   G + Q GS + +Y +P + +VA F+G   +N+L   V + 
Sbjct: 192 VTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQ--VNYLSCEVKD- 248

Query: 256 GFVDFGEFRLKLLPDQFEVLGEL----GYVGREVIFGIRPEDL 294
                   RL+ L  + +   +L    GY G  +   +RPE L
Sbjct: 249 ------RARLQTLLGEVQSSSDLPKAAGYRGELL---LRPEQL 282


Lambda     K      H
   0.323    0.142    0.406 

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: 317
Number of extensions: 18
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: 372
Length of database: 342
Length adjustment: 29
Effective length of query: 343
Effective length of database: 313
Effective search space:   107359
Effective search space used:   107359
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 (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