GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Caulobacter crescentus NA1000

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  387 bits (995), Expect = e-112
 Identities = 209/504 (41%), Positives = 316/504 (62%), Gaps = 10/504 (1%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           LL +  + K+FPGV+AL    L V  G V AL+GENGAGKST++K+L+  +  DAGT+ +
Sbjct: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62

Query: 64  LGKETT-FTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122
            G+       P   Q+ GI  I+QE NL P+L++AEN++LGRE   R G +DW  + A+A
Sbjct: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGRE-PRRLGLVDWSRLRADA 121

Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182
             LL  L L    D  V  L++ +QQMVEIAK ++  +++IIMDEPT AL+  E + L  
Sbjct: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181

Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242
           +I  LK++   ++Y+SHR+ E+  +CD  TV RDG+F+A  +VA +    ++ +MVGR +
Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241

Query: 243 EDQYPHLDKAPGDIRLKVDN-------LCGPG-VNDVSFTLRKGEILGVSGLMGAGRTEL 294
           E +     + PG + LKV+        L  PG +  VSF  R GEI+G++GL+GAGRT+L
Sbjct: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301

Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354
            ++++GA P  +G V +D   +  RSP+D +  GI+ + EDRK+ G  L  S++ N+SL 
Sbjct: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361

Query: 355 ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414
           +L+  S  G  +    E+  V  + +   +K    E AIG LSGGNQQKV + R +   P
Sbjct: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421

Query: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474
           KVLI+DEPTRG+D+GAK E++Q+++     G++++++SSE+ EV+ +SDRI+V  EG + 
Sbjct: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481

Query: 475 GEFTREQATQEVLMAAAVGKLNRV 498
            +   + AT+E LMA      +RV
Sbjct: 482 ADLDAQTATEEGLMAYMATGTDRV 505


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: 654
Number of extensions: 43
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: 515
Length adjustment: 34
Effective length of query: 467
Effective length of database: 481
Effective search space:   224627
Effective search space used:   224627
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.

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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