Alignments for a candidate for rbsA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Klebsiella michiganensis M5al

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate BWI76_RS00660 BWI76_RS00660 ABC transporter

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS00660
          Length = 503

 Score =  418 bits (1075), Expect = e-121
 Identities = 213/492 (43%), Positives = 321/492 (65%), Gaps = 3/492 (0%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           LL LKGI K FPGV+AL    L+++PG+V AL+GENGAGKST++KV+TGIY  + G +L+
Sbjct: 7   LLSLKGITKVFPGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEILY 66

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREF-VNRFGKIDWKTMYAEA 122
                    P+S+ + GI  IHQE  L  +L++ ENIF+G+        K+DW  M+ +A
Sbjct: 67  KAIPIQLPNPESAHKVGITAIHQETVLFDELSVTENIFVGQYLHTGLLKKLDWPAMHRKA 126

Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182
            ++L +L ++      +  LSI  + MV IA+ LSFE++V+I+DEPT AL+  E    ++
Sbjct: 127 SEILTRLEVQIDPRATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEILEFYQ 186

Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242
           ++  LK  G+ I++ISH+  EIFE+ D  T+ RDG +++   +  +TE+ ++ MMVGR +
Sbjct: 187 IVERLKQDGKAILFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERMVAMMVGRAI 246

Query: 243 EDQYPHLDKAPGDIRLKVDNLCGP-GVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGA 301
              YP +D  PG+  L+V +LC P     +SF+LRKGEILG  GL+GAGRTELM+ L G 
Sbjct: 247 TQTYPKVDCIPGETVLEVKDLCHPTEFAHISFSLRKGEILGFYGLVGAGRTELMQALSGV 306

Query: 302 LPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSR 361
              +SG + L G  +  R P D ++ GIV + E+R++ G ++ + + +N+SL  L   + 
Sbjct: 307 SHPSSGDIVLKGKPMRFRQPADAISAGIVCVPEERQKQGAIIALPIAQNISLPQLSKLN- 365

Query: 362 AGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDE 421
            GG L  A E +   ++     VK  S  QA+  LSGGNQQKV I + L T P+V+ILDE
Sbjct: 366 PGGVLNDAREWRLADEYASRLQVKAFSWRQAVETLSGGNQQKVVIGKWLATHPEVIILDE 425

Query: 422 PTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQ 481
           PT+G+D+G+K  ++Q +++  + GL++I+VSSE+PEV+GM+DRIIVMHEG +  E+   +
Sbjct: 426 PTKGIDIGSKAAVHQFMSELVSQGLAVIMVSSELPEVMGMADRIIVMHEGLMVAEYRAGE 485

Query: 482 ATQEVLMAAAVG 493
           AT E +++AA G
Sbjct: 486 ATAETIVSAASG 497



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 61/235 (25%), Positives = 105/235 (44%), Gaps = 14/235 (5%)

Query: 266 PGVN---DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV    +V   L  G++  + G  GAG++ L+KV+ G      G +      +   +P+
Sbjct: 18  PGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEILYKAIPIQLPNPE 77

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHAD---EQQAVSDFI 379
                GI  I ++     L   +SV EN+ +    +     G LK  D     +  S+ +
Sbjct: 78  SAHKVGITAIHQETV---LFDELSVTENIFVGQYLHT----GLLKKLDWPAMHRKASEIL 130

Query: 380 RLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLIN 439
               V+       +  LS   +  VAIAR L    +V+ILDEPT  +      E YQ++ 
Sbjct: 131 TRLEVQIDP-RATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEILEFYQIVE 189

Query: 440 QFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           + K DG +I+ +S +  E+  ++D   ++ +G           T+E ++A  VG+
Sbjct: 190 RLKQDGKAILFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERMVAMMVGR 244


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: 594
Number of extensions: 20
Number of successful extensions: 8
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: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources