GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaK in Klebsiella michiganensis M5al

Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate BWI76_RS06435 BWI76_RS06435 MFS transporter

Query= SwissProt::Q51955
         (448 letters)



>FitnessBrowser__Koxy:BWI76_RS06435
          Length = 454

 Score =  445 bits (1144), Expect = e-129
 Identities = 214/430 (49%), Positives = 298/430 (69%), Gaps = 2/430 (0%)

Query: 12  LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71
           LDV+  IN  PLSR+Q  VVLL F ++ LDG D A MGFIAP L QEWG+    LG V+S
Sbjct: 7   LDVRELINANPLSRFQKLVVLLGFCVIALDGFDIAIMGFIAPTLKQEWGVSNHELGFVIS 66

Query: 72  AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131
           AALIG+  GA+ SGPLAD  GRK +++ +V  FG +++A+A + N++Q++V RFLTGLGL
Sbjct: 67  AALIGLALGAIFSGPLADWLGRKKIIINSVFFFGFWTIATALSQNIEQMMVFRFLTGLGL 126

Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191
           GA MPN  TL+SEY PER +S L+T +FCGF  G A GGF ++ +IP +GWHSL+++GG+
Sbjct: 127 GAAMPNIGTLVSEYAPERQRSFLITIIFCGFTFGAAAGGFSASWLIPQFGWHSLMLLGGI 186

Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAARS 251
           LPLL A VL+  LPES RFLVV+    ++IR+ L  + P  + +   FS+P Q   A  +
Sbjct: 187 LPLLFAPVLIWLLPESVRFLVVKRAPAERIRRILQRLYPGQIPDEAEFSLPTQPVQA--N 244

Query: 252 VFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFGG 311
              ++ S  Y  G+M+LWL YFMGL +VYLL SWLPTL+++ G ++ QAA + A++Q GG
Sbjct: 245 AMRIVLSRQYRFGSMMLWLVYFMGLFLVYLLGSWLPTLVKEVGLTVSQAAVMTAMYQAGG 304

Query: 312 VLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQS 371
            L ++  GW MDR NPH+ +G+ Y + G+F  A+G +  +  ++  L  I+G C+NGA +
Sbjct: 305 TLGSLFAGWLMDRINPHRALGLIYAVGGLFTMAMGYAAASFALICLLAFISGACLNGANT 364

Query: 372 AMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAAL 431
            M +L+AR+YPT+ RATG SWM G+GR GAIL A++GA +L L  +FE V   L +PAA+
Sbjct: 365 GMNALSARYYPTEARATGSSWMHGVGRLGAILSAFAGAEMLALNISFESVFLILGIPAAI 424

Query: 432 ATVGVIVKGL 441
              G+  KG+
Sbjct: 425 TVAGLAAKGV 434


Lambda     K      H
   0.325    0.140    0.424 

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: 629
Number of extensions: 33
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: 448
Length of database: 454
Length adjustment: 33
Effective length of query: 415
Effective length of database: 421
Effective search space:   174715
Effective search space used:   174715
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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