GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Klebsiella michiganensis M5al

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS27035 BWI76_RS27035 xylose ABC
           transporter ATP-binding protein
          Length = 513

 Score =  447 bits (1149), Expect = e-130
 Identities = 247/504 (49%), Positives = 341/504 (67%), Gaps = 4/504 (0%)

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

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
            + G       I D+E  GI IIHQELALV  L++ ENIFLG E++ +G++ ++    R 
Sbjct: 64  IFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMTLRC 123

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

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

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

Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364
           E    +FG   G R  G + IDG+PV + T ++AI  G+A V EDRK  G+V    +  N
Sbjct: 302 EAVQCLFGVWPG-RWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKN 360

Query: 365 TTLANL-AGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
            TLA L       S +DD  E         RL+I++S        LSGGNQQK +L++ L
Sbjct: 361 ITLAALNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAILARCL 420

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
             NP +LILDEPTRGID+GAKYEIY +INQL   G  V++ISSE+PE+LG  DR+ VM+E
Sbjct: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480

Query: 484 GRIVAELPKGEASQESIMRAIMRS 507
           G++ A L     +QE +M A +RS
Sbjct: 481 GKLKANLINQGLTQEQVMEAALRS 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: 686
Number of extensions: 37
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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