GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Klebsiella michiganensis M5al

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate BWI76_RS01840 BWI76_RS01840 ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Koxy:BWI76_RS01840
          Length = 369

 Score =  295 bits (754), Expect = 2e-84
 Identities = 168/365 (46%), Positives = 224/365 (61%), Gaps = 19/365 (5%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA + L +VTK +     GD+V  ++I+L+I DGEF+V VGPSGCGKST LRM+AGLETV
Sbjct: 1   MASVQLRNVTKAW-----GDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIAGLETV 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           T G+L + D  +N V   +R I MVFQSYALYPH SV  NMSFGL+ + G   + I QRV
Sbjct: 56  TSGDLLIGDTRMNDVPPAERGIGMVFQSYALYPHLSVAENMSFGLKLA-GAKKELINQRV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
            +  ++L ++ LL+RKP  LSGGQ+QRVA+GR +V +P VFL+DEPLSNLDA LR +MR 
Sbjct: 115 TQVAEVLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRI 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+ RL   LG T +YVTHDQ EAMT+ D++ VLD G + QVG PL+ YH P + FVAGFI
Sbjct: 175 EISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFI 234

Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLS-------GATRDQLGGASGLTLGIRPEDVTVGE 293
           G P MN     ++         + P          + R Q+G  + ++LGIRPE +   +
Sbjct: 235 GSPKMNFLPVKVTATAIEQVQVELPNRQQVWLPVDSARVQVG--ANMSLGIRPEHLLPSD 292

Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353
                 T + EV VVE  G+E  +H++     +   +         VE G    +  P +
Sbjct: 293 --IADVTLEGEVQVVEQLGHETQIHIQIPSIRQNLVYRQNDV--VLVEEGATFAIGLPPE 348

Query: 354 AIHLF 358
             HLF
Sbjct: 349 RCHLF 353


Lambda     K      H
   0.316    0.136    0.384 

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: 400
Number of extensions: 24
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: 383
Length of database: 369
Length adjustment: 30
Effective length of query: 353
Effective length of database: 339
Effective search space:   119667
Effective search space used:   119667
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: 42 (22.0 bits)
S2: 50 (23.9 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