GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pantoea rwandensis LMG 26275

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_084932971.1 HA51_RS05635 xylose ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_002095475.1:WP_084932971.1
          Length = 506

 Score =  427 bits (1098), Expect = e-124
 Identities = 233/500 (46%), Positives = 326/500 (65%), Gaps = 12/500 (2%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDA--GTL 61
           LL++  I K F  VKAL   +L +  G VM+L GENG+GKST+MK+L G+Y      G +
Sbjct: 2   LLEMNHITKRFGAVKALDDISLRLDAGEVMSLCGENGSGKSTLMKILCGLYPHGDFDGEI 61

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121
            + G        + ++  GI IIHQEL L+ QLT+ ENIFLG E + RFG +D +TM   
Sbjct: 62  QFAGDRIQAQTIRDTERKGIVIIHQELALVRQLTVMENIFLGAE-LGRFGLVDDETMTLR 120

Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181
             +LLA++ L    D  VG+L +G QQ+VEIA+ L+ + +++I+DEPT +LT+ ETE L 
Sbjct: 121 CQQLLARVKLDVAPDTKVGELGLGQQQLVEIARALNKQVRLLILDEPTSSLTEQETEVLL 180

Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
            +I  L+  G   +YISH++ E+  I D + V RDGQ IA R  A L+ED +I MMVGR+
Sbjct: 181 SIINNLREHGIACIYISHKLNEVKAISDTICVIRDGQHIATRPAAGLSEDDIITMMVGRE 240

Query: 242 LEDQYPHLDKAPGDIRLKVDNLCG--------PGVNDVSFTLRKGEILGVSGLMGAGRTE 293
           L   YPH     G+  L+V NL            VN+VSF+L++GEILG++GL+GAGRTE
Sbjct: 241 LTALYPHQPHEIGETILEVKNLTAWHPVNRHVRRVNNVSFSLKRGEILGIAGLVGAGRTE 300

Query: 294 LMKVLYGALP-RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMS 352
            ++ L+G  P R  G + ++G  V     ++ +A+GI  + EDRK+DG+V  M V +N++
Sbjct: 301 TVQCLFGVWPGRWQGDIAINGKLVKIHDCREAIAHGIAMVPEDRKKDGIVPLMGVGKNIT 360

Query: 353 LTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMT 412
           L AL  FS    ++  A EQQA++D IR   VKT S E AIG LSGGNQQK  +A+ L+ 
Sbjct: 361 LAALDQFSHRLSTVDEAAEQQAINDAIRRLRVKTSSPELAIGRLSGGNQQKAILAKCLLL 420

Query: 413 RPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGH 472
            PK+LILDEPTRG+DVGA++EIY LIN     G+++I++SSE+PEVLG+SDR++VMHEG 
Sbjct: 421 NPKILILDEPTRGIDVGARQEIYLLINALVQQGIAVIVISSELPEVLGLSDRVLVMHEGQ 480

Query: 473 LSGEFTREQATQEVLMAAAV 492
           +  +      TQE +M AA+
Sbjct: 481 IKADLINNNLTQEQVMEAAL 500


Lambda     K      H
   0.318    0.137    0.380 

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: 650
Number of extensions: 33
Number of successful extensions: 9
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: 501
Length of database: 506
Length adjustment: 34
Effective length of query: 467
Effective length of database: 472
Effective search space:   220424
Effective search space used:   220424
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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