GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Klebsiella michiganensis M5al

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  372 bits (954), Expect = e-107
 Identities = 218/501 (43%), Positives = 303/501 (60%), Gaps = 13/501 (2%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L    I K FPGV+AL  V L    G VHALMGENGAGKSTLMK L G Y  D G    +
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGA-IRV 64

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133
            G+ VQ      A   G+++I+QEL+L P+++VAENI+LGR   + G V    + R    
Sbjct: 65  KGEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQD 124

Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193
            L +L    S    V  LSIA +Q+VEIA+AV + A I++MDEPT+ L+  E   LF +I
Sbjct: 125 LLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTII 184

Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSG 253
           R LR +G AI+YISH+M EI  + D ++V RDG +VG+      ++ +L+  MVGR+L+ 
Sbjct: 185 RDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRELTQ 244

Query: 254 FYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGA 313
            + K    A+  EV L+VR+++        +F +R GE+LG+AGLVGAGR+E+   +FG 
Sbjct: 245 LFPK-FNNAIGEEV-LTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGM 302

Query: 314 DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLI 373
           +    GEV I         + +    P  AI+ G+A LTEDRK  GLFL  SV EN++++
Sbjct: 303 EKADSGEVLIDG-------MPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIV 355

Query: 374 VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQP 433
                    G +          E I  L I+       +  LSGGNQQKV+++R L  QP
Sbjct: 356 KMPEYIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQP 415

Query: 434 RVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTLA 493
           ++LILDEPTRG+D+GAK+EIY LI+ LA  GVA++M+SSELPE++G+ DRV+VM EG + 
Sbjct: 416 KILILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRIT 475

Query: 494 GEVRPAGSAAETQERIIALAT 514
           G +    +    QE I++LA+
Sbjct: 476 GILDKEDA---DQETILSLAS 493


Lambda     K      H
   0.320    0.136    0.382 

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: 576
Number of extensions: 36
Number of successful extensions: 9
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: 540
Length of database: 494
Length adjustment: 35
Effective length of query: 505
Effective length of database: 459
Effective search space:   231795
Effective search space used:   231795
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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