GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proW in Klebsiella michiganensis M5al

Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate BWI76_RS22070 BWI76_RS22070 proline/betaine ABC transporter permease ProW

Query= SwissProt::P14176
         (354 letters)



>FitnessBrowser__Koxy:BWI76_RS22070
          Length = 354

 Score =  649 bits (1673), Expect = 0.0
 Identities = 323/354 (91%), Positives = 339/354 (95%)

Query: 1   MADQNNPWDTTPAADSAAQSADAWGTPTTAPTDGGGADWLTSTPAPNVEHFNILDPFHKT 60
           MADQ+NPWDT PAADSAAQSADAWGT T APT+GG ADWL+S PAP  EHFNI+DPFH T
Sbjct: 1   MADQSNPWDTAPAADSAAQSADAWGTSTPAPTNGGSADWLSSAPAPQPEHFNIMDPFHNT 60

Query: 61  LIPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQI 120
           LIPLDSWVT GIDWVV HFRP+FQG+RVPVDYIL+ FQQLLLGMPAPVAII+F+LIAWQI
Sbjct: 61  LIPLDSWVTHGIDWVVMHFRPLFQGIRVPVDYILSAFQQLLLGMPAPVAIIIFSLIAWQI 120

Query: 121 SGVGMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKII 180
           S VGMG ATL+SLIAIGAIGAWSQAMVTLALVLTALLFC++IGLPLGIWLARSPRAAKII
Sbjct: 121 SSVGMGAATLISLIAIGAIGAWSQAMVTLALVLTALLFCMLIGLPLGIWLARSPRAAKII 180

Query: 181 RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEA 240
           RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPI+RLTILGINQVPADLIEA
Sbjct: 181 RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIVRLTILGINQVPADLIEA 240

Query: 241 SRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR 300
           SRSFGASPRQ+LFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR
Sbjct: 241 SRSFGASPRQLLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR 300

Query: 301 LDMGLATVGGVGIVILAIILDRLTQAVGRDSRSRGNRRWYTTGPVGLLTRPFIK 354
           LDMGLATVGGVGIVILAIILDRLTQAVGRDSRSRGNRRWY TGP+GL+TRPF K
Sbjct: 301 LDMGLATVGGVGIVILAIILDRLTQAVGRDSRSRGNRRWYATGPLGLITRPFCK 354


Lambda     K      H
   0.326    0.141    0.435 

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: 596
Number of extensions: 22
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: 354
Length of database: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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: 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