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_084932744.1 HA51_RS05190 ribose ABC transporter ATP-binding protein RbsA

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_002095475.1:WP_084932744.1
          Length = 502

 Score =  840 bits (2171), Expect = 0.0
 Identities = 428/494 (86%), Positives = 464/494 (93%)

Query: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60
           M+ LLQLKGI+K+FPGVKAL+GA+L VYPGRVMALVGENGAGKSTMMKVLTGIY+ DAG+
Sbjct: 1   MQPLLQLKGIEKSFPGVKALNGASLAVYPGRVMALVGENGAGKSTMMKVLTGIYSMDAGS 60

Query: 61  LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120
           L WLGK+  F+GPK+SQEAGIGIIHQELNLIPQLT+AENIFLGREFVNRFG+I+W  MYA
Sbjct: 61  LQWLGKDVAFSGPKASQEAGIGIIHQELNLIPQLTVAENIFLGREFVNRFGRIEWNRMYA 120

Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
           EAD LL +LNLRF S KLVGDLSIGDQQMVEIAKVLSFES+VIIMDEPTDALTDTET SL
Sbjct: 121 EADALLHRLNLRFNSHKLVGDLSIGDQQMVEIAKVLSFESQVIIMDEPTDALTDTETLSL 180

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           FRVI ELK+QG GIVYISHRMKEIFEICDDVTVFRDGQFIAER V+ L+E+SLIEMMVGR
Sbjct: 181 FRVINELKAQGCGIVYISHRMKEIFEICDDVTVFRDGQFIAERAVSDLSEESLIEMMVGR 240

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300
           KLEDQYPH+D+APGDIRL V++L GPGV++VSF LRKGEILG+SGLMGAGRTELMKVLYG
Sbjct: 241 KLEDQYPHIDQAPGDIRLTVEHLSGPGVDNVSFNLRKGEILGISGLMGAGRTELMKVLYG 300

Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360
           ALPR+ G VTL+G E++TRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS
Sbjct: 301 ALPRSKGTVTLNGREIMTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360

Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420
            A G+LKH++EQ AV DFIRLFNVKTPSMEQ IGLLSGGNQQKVAIARGLMTRP VLILD
Sbjct: 361 HATGNLKHSEEQLAVGDFIRLFNVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILD 420

Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480
           EPTRGVDVGAKKEIYQLINQFKA+GLSIILVSSEMPEVLGMSDRI+VMHEGHLSGEF+RE
Sbjct: 421 EPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSRE 480

Query: 481 QATQEVLMAAAVGK 494
           QATQE LMAAAVGK
Sbjct: 481 QATQESLMAAAVGK 494



 Score = 94.7 bits (234), Expect = 7e-24
 Identities = 65/237 (27%), Positives = 117/237 (49%), Gaps = 9/237 (3%)

Query: 15  PGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPK 74
           PGV  +S    N+  G ++ + G  GAG++ +MKVL G   R  GT+   G+E     P+
Sbjct: 266 PGVDNVS---FNLRKGEILGISGLMGAGRTELMKVLYGALPRSKGTVTLNGREIMTRSPQ 322

Query: 75  SSQEAGIGIIHQELN---LIPQLTIAENIFLG--REFVNRFGKIDWKTMYAEADKLLAKL 129
                GI  I ++     L+  +++ EN+ L   R F +  G +            +   
Sbjct: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSHATGNLKHSEEQLAVGDFIRLF 382

Query: 130 NLRFKS-DKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELK 188
           N++  S ++ +G LS G+QQ V IA+ L     V+I+DEPT  +     + ++++I + K
Sbjct: 383 NVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILDEPTRGVDVGAKKEIYQLINQFK 442

Query: 189 SQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLEDQ 245
           ++G  I+ +S  M E+  + D + V  +G    E      T++SL+   VG++  ++
Sbjct: 443 AEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSREQATQESLMAAAVGKQHSEE 499


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: 905
Number of extensions: 26
Number of successful extensions: 5
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: 501
Length of database: 502
Length adjustment: 34
Effective length of query: 467
Effective length of database: 468
Effective search space:   218556
Effective search space used:   218556
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