GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Rhodobacter johrii JA192

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  375 bits (963), Expect = e-108
 Identities = 208/497 (41%), Positives = 312/497 (62%), Gaps = 5/497 (1%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           E +L ++ + + F  V+ L     ++ PG V AL+GENGAGKST MK+L G     AG +
Sbjct: 3   EPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEV 62

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121
           L  G+   F   + ++ AG+ +IHQE NL   LT+ ENIFLGRE + R   +D + M AE
Sbjct: 63  LLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRE-LKRGPFLDHRAMQAE 121

Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181
           + +LL +L+        V  LS+ ++QMVEIAK L  +++V+IMDEPT  LT  ET++L 
Sbjct: 122 SRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181

Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
             +  L++ G  I+Y SH++ E+  I D VTV RDG+ +       L+ED + E MVGR+
Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRE 241

Query: 242 LEDQYPHLDKAPGDIRLKVDNLCGPG-VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300
           L   +P       +  L+V  L  PG V D SFTLR+GE+LG +GL+G+GRTELM+ + G
Sbjct: 242 LSGLFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVG 301

Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360
             P T G V ++G  +   S     A G+VY++EDRK  GL+LG  + EN++L AL  F 
Sbjct: 302 LRPAT-GEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFG 360

Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420
           R    +  A E++A++  I  F+++      + G LSGGNQQK+ +A+ ++  P+V+I+D
Sbjct: 361 RV--LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIID 418

Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480
           EPTRG+DVG K++IY  I +  A+G S+I+VSSE+PEV+G+++R++VM  G ++GE   E
Sbjct: 419 EPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGE 478

Query: 481 QATQEVLMAAAVGKLNR 497
             T+E ++  A+G  +R
Sbjct: 479 AITEENIVRLAMGLNHR 495


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: 621
Number of extensions: 29
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: 501
Length of database: 499
Length adjustment: 34
Effective length of query: 467
Effective length of database: 465
Effective search space:   217155
Effective search space used:   217155
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