GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate H281DRAFT_06298 H281DRAFT_06298 L-arabinose ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__Burk376:H281DRAFT_06298
          Length = 519

 Score =  390 bits (1002), Expect = e-113
 Identities = 211/494 (42%), Positives = 311/494 (62%), Gaps = 10/494 (2%)

Query: 14  LEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQ 73
           L    I K FPGV+ALD V+ +V    +H LMGENGAGKSTLLK L G YQ DSG ++  
Sbjct: 12  LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 71

Query: 74  GKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKAI 133
           GKEV F SA  ++  GI+++HQEL  V   +V +N+ LG+ P    +V++    +  +  
Sbjct: 72  GKEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSFGWVNKRDAKRFVRER 131

Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193
            + + + +DP A++  LS++Q QM+EI KA   NA+++ +DEPTSSL+ +E   LF ++R
Sbjct: 132 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 191

Query: 194 KLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQP-LEGLDMDKIIAMMVGRSLNQ 252
            L+     ++YISH+M+EI++LCD  TI RDG+ IA+ P LEG+  D I++ MVGR ++ 
Sbjct: 192 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVSRDTIVSEMVGREISD 251

Query: 253 RFPDKENKPGDVILEVRHLT--SLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
            +   E   G+V    + +   +L QP+    SF++ +GEI+G  GLVGA R++++  ++
Sbjct: 252 IYNYSERPLGEVRFAAKAIEGHALSQPA----SFEVRRGEIVGFFGLVGAGRSELMHLVY 307

Query: 311 GIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           G   K  G + L GK I   +A EAI HG  L  E+R+  GI A   +  N  IS  R+Y
Sbjct: 308 GTEHKKGGELVLDGKTIRVKSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 367

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE--IL 428
                 LD  +        I  +++KTP  R +I  LSGGNQQK I+ RW L +P+  ++
Sbjct: 368 LRAGVFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRW-LAEPDLKVV 426

Query: 429 MLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIV 488
           +LDEPTRGIDVGAK EIY +I +LA++G  I++ISSE+PE+LG++DRI+VM  G ++G +
Sbjct: 427 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRIAGEL 486

Query: 489 DTKTTTQNEILRLA 502
             K  T+  +L LA
Sbjct: 487 SRKDATEQAVLSLA 500


Lambda     K      H
   0.319    0.137    0.388 

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: 579
Number of extensions: 24
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: 506
Length of database: 519
Length adjustment: 35
Effective length of query: 471
Effective length of database: 484
Effective search space:   227964
Effective search space used:   227964
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 (21.7 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