Alignments for a candidate for BPHYT_RS16930 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Escherichia coli BW25113

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__Keio:17628
          Length = 513

 Score =  349 bits (896), Expect = e-100
 Identities = 204/500 (40%), Positives = 312/500 (62%), Gaps = 13/500 (2%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQI- 74
           L    I K+F  V+A+ N+    + G++ +L GENG+GKSTL+K+L G Y   S + +I 
Sbjct: 5   LEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEII 64

Query: 75  --GEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQA 132
             GE+  A     D+   G+A+IHQEL LV E+TV EN+FLG+     G+++  ++  + 
Sbjct: 65  FAGEEIQA-SHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLRC 123

Query: 133 LTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 192
             LL  ++  I P  +VG L LGQ+QLVEIAKAL++   ++  DEPT+SL+ +E   L+ 
Sbjct: 124 QKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLD 183

Query: 193 IIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRD 252
           II  L+  G   +Y+SH++ EV  I + + V +DG+++ T  + + ++ D ++T MVGR+
Sbjct: 184 IIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGT-RDAAGMSEDDIITMMVGRE 242

Query: 253 IQDIYDYRPRERGDVALQVKGLLG---PGLH----EPVSFQVHKGEILGLFGLVGAGRTE 305
           +  +Y   P   GD  L+++ L        H      VSF + +GEILG+ GLVGAGRTE
Sbjct: 243 LTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTE 302

Query: 306 LLRLLSGL-ERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENIN 364
            ++ L G+   Q EG + +  K++ +R+ + AIA G+ + PEDRK++GI+P+ +VG+NI 
Sbjct: 303 TIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNIT 362

Query: 365 ISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSM 424
           ++A    +     L    E+    + I+ LKVKT +    I  LSGGNQQKAIL R L +
Sbjct: 363 LAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLLL 422

Query: 425 PMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGA 484
             ++L+LDEPTRGIDIGAK EIY++I+ L   GIAVIV+SS+L EV+G+SDR+LV+ EG 
Sbjct: 423 NPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEGK 482

Query: 485 MRGELSRDQANESNLLQLAL 504
           ++  L      +  +++ AL
Sbjct: 483 LKANLINHNLTQEQVMEAAL 502



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 56/230 (24%), Positives = 111/230 (48%), Gaps = 9/230 (3%)

Query: 283 VSFQVHKGEILGLFGLVGAGRTELLRLLSGL--ERQREGSLVLHDKELKLRSPRDAIAAG 340
           V  +++ GEI+ L G  G+G++ L+++L G+      EG ++   +E++    RD    G
Sbjct: 23  VCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEEIQASHIRDTERKG 82

Query: 341 VLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPT 400
           + +  ++     ++   +V ENI +    +H+ +   +  D       K +  + +   +
Sbjct: 83  IAIIHQEL---ALVKELTVLENIFLGNEITHNGI---MDYDLMTLRCQKLLAQVSLSI-S 135

Query: 401 AGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAV 460
              ++  L  G QQ   + + L+  +++L+LDEPT  +     + +  II +L   GIA 
Sbjct: 136 PDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQHGIAC 195

Query: 461 IVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQRVA 510
           I +S  L EV  ISD I V+ +G   G       +E +++ + + R+  A
Sbjct: 196 IYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRELTA 245


Lambda     K      H
   0.320    0.138    0.391 

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: 677
Number of extensions: 38
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 514
Length of database: 513
Length adjustment: 35
Effective length of query: 479
Effective length of database: 478
Effective search space:   228962
Effective search space used:   228962
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources