GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Escherichia coli BW25113

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Keio:17628
          Length = 513

 Score =  443 bits (1139), Expect = e-129
 Identities = 245/507 (48%), Positives = 342/507 (67%), Gaps = 10/507 (1%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +LEM+NITKTF  VKA++NV L++  GEI +L GENG+GKSTLMKVL G+YP G+YEGEI
Sbjct: 4   LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
            + G       I D+E  GI IIHQELALV  L++ ENIFLGNE+  NG++ +     R 
Sbjct: 64  IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLRC 123

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           ++LL +V L  SP+T + D+G+G+QQLVEIAKAL+K V+LLILDEPTASL E ++  LL+
Sbjct: 124 QKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLD 183

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           ++ + +  G+  I I+HKLNEV+ ++D I V+RDG  + T D     +SED II  MVGR
Sbjct: 184 IIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDA--AGMSEDDIITMMVGR 241

Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304
           +L   YP      G+ IL +++  A+H  +R  + ++D++ ++++GE++GIAGL+GAGRT
Sbjct: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301

Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364
           E    +FG   G +  G + IDGK VD+   ++AI  G+A V EDRK  G+V    +  N
Sbjct: 302 ETIQCLFGVWPG-QWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360

Query: 365 TTLANL----AGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
            TLA L     G+S+   +DD  E K   +   +L++++S        LSGGNQQK +L+
Sbjct: 361 ITLAALNKFTGGISQ---LDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILA 417

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           + L  NP +LILDEPTRGID+GAKYEIY +INQL   G  V++ISSE+PE+LG  DR+ V
Sbjct: 418 RCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLV 477

Query: 481 MNEGRIVAELPKGEASQESIMRAIMRS 507
           M+EG++ A L     +QE +M A +RS
Sbjct: 478 MHEGKLKANLINHNLTQEQVMEAALRS 504


Lambda     K      H
   0.316    0.135    0.374 

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: 682
Number of extensions: 38
Number of successful extensions: 8
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: 512
Length of database: 513
Length adjustment: 35
Effective length of query: 477
Effective length of database: 478
Effective search space:   228006
Effective search space used:   228006
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: 41 (21.6 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