GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Escherichia coli BW25113

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Keio:17628
          Length = 513

 Score =  359 bits (921), Expect = e-103
 Identities = 208/487 (42%), Positives = 299/487 (61%), Gaps = 14/487 (2%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71
           LL ++NI KTF  V+A+  V L   AGE+ +L GENG+GKSTLMK+L G Y      GE 
Sbjct: 4   LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
              G+ +Q    +     G+A+I+QEL+L   L+V ENI+LG  +   G++    M   C
Sbjct: 64  IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLRC 123

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              LA++    SP   V  L + Q+QLVEIA+A++ + R+L++DEPT  L+  ET  L  
Sbjct: 124 QKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLD 183

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           +IR L+  G+A +YISH++ E+  ++D + V+RDG  +GT D A +S+  ++ MMVGR+L
Sbjct: 184 IIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGREL 243

Query: 252 SGFYTK---THGQAVEREVMLSVRDVADG--RRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306
           +  Y     T G  + R   L+     +   +RV   SF L+ GE+LG+AGLVGAGRTE 
Sbjct: 244 TALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTET 303

Query: 307 ARLVFGA-DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQS 365
            + +FG    +  G++ I      G  V +     +QAI  GIA + EDRK  G+    +
Sbjct: 304 IQCLFGVWPGQWEGKIYI-----DGKQVDIR--NCQQAIAQGIAMVPEDRKRDGIVPVMA 356

Query: 366 VHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVML 425
           V +NI L    +   G+ +L+  A ++   E+I  L ++ +   + +G LSGGNQQK +L
Sbjct: 357 VGKNITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAIL 416

Query: 426 SRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVL 485
           +R L + PR+LILDEPTRG+DIGAK EIY+LIN L Q G+A+++ISSELPEV+GL DRVL
Sbjct: 417 ARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVL 476

Query: 486 VMREGTL 492
           VM EG L
Sbjct: 477 VMHEGKL 483



 Score = 84.3 bits (207), Expect = 1e-20
 Identities = 63/247 (25%), Positives = 125/247 (50%), Gaps = 10/247 (4%)

Query: 8   STKAPLLALRNICKTFPGVRALRKVELTAYA---GEVHALMGENGAGKSTLMKILSGAYT 64
           +T   +L + ++    P  R +++V   +++   GE+  + G  GAG++  ++ L G + 
Sbjct: 253 TTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTETIQCLFGVWP 312

Query: 65  ADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGRALQRRGL 121
               G+ +IDG++V I   Q A   G+A++ ++     + P ++V +NI L    +  G 
Sbjct: 313 GQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNITLAALNKFTGG 372

Query: 122 VARGDMV---RACAPTLARLGADFS-PAANVASLSIAQRQLVEIARAVHFEARILVMDEP 177
           +++ D     +    ++ +L    S P   +  LS   +Q   +AR +    RIL++DEP
Sbjct: 373 ISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLLLNPRILILDEP 432

Query: 178 TTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL 237
           T  +       ++ LI QL  +G+A++ IS  + E+  L+DRV V+ +G     L   +L
Sbjct: 433 TRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEGKLKANLINHNL 492

Query: 238 SQAALVK 244
           +Q  +++
Sbjct: 493 TQEQVME 499



 Score = 67.4 bits (163), Expect = 1e-15
 Identities = 65/236 (27%), Positives = 107/236 (45%), Gaps = 19/236 (8%)

Query: 287 LRAGEVLGLAGLVGAGRTELARLVFGA--DARTRGEVRIANPAGSGGLVTLPAGGPRQAI 344
           L AGE++ L G  G+G++ L +++ G        GE+  A          + A   R   
Sbjct: 27  LNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEE-------IQASHIRDTE 79

Query: 345 DAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIR 404
             GIA + ++     L  + +V ENI L     +    G ++      R  + +  + + 
Sbjct: 80  RKGIAIIHQEL---ALVKELTVLENIFL---GNEITHNGIMDYDLMTLRCQKLLAQVSLS 133

Query: 405 VAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSG 464
           ++     VG L  G QQ V +++ L  Q R+LILDEPT  +     S +  +I  L Q G
Sbjct: 134 IS-PDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQHG 192

Query: 465 VAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAA 520
           +A + IS +L EV  + D + V+R+G   G    AG    +++ II +  G    A
Sbjct: 193 IACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGM---SEDDIITMMVGRELTA 245


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: 553
Number of extensions: 24
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 540
Length of database: 513
Length adjustment: 35
Effective length of query: 505
Effective length of database: 478
Effective search space:   241390
Effective search space used:   241390
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