GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Tistlia consotensis USBA 355

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IUD1
         (522 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  315 bits (806), Expect = 3e-90
 Identities = 188/496 (37%), Positives = 281/496 (56%), Gaps = 7/496 (1%)

Query: 11  SPLLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGM 69
           +PLL L G+ +R+   + LD +D  LRPG+V  L GENGAGKST+  +I G +  S G  
Sbjct: 21  APLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEF 80

Query: 70  MLDGQPYAPASRTQAEGLGIRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAA 129
              G+P    S   A GLGI  V QE +L+P +++ ENLFL     R G +DR+ L + A
Sbjct: 81  RFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRA 140

Query: 130 RAQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLF 189
            A ++ +G   L P   V  L    QQMVEIA+        LILDEPTA LT RE   LF
Sbjct: 141 DAILKRLGF-PLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLF 199

Query: 190 SRIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQLMAGEL 249
             IE+++A+GV +IYI+HRL E++RI DRI VLRDG+ V   D       +LV+LM G +
Sbjct: 200 KLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRV 259

Query: 250 TKVDLDAEHRRIGAPVLRIRGLGRAP-VVHPASLALHAGEVLGIAGLIGSGRTELLRLIF 308
                     + G  +L +  L  A   V  ASL++ AGE++G+AGL+GSG++E+ R  F
Sbjct: 260 YDELFPKVRFKPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACF 319

Query: 309 GADRAEQGEIFIGDSQEPARIRSPKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLAN-- 366
           G ++  +G + +    E    + PK  +K G   V  DR+ +GL++ + +  N SL +  
Sbjct: 320 GLEKIAEGHVRL--KGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLT 377

Query: 367 LGSVSRGGMLDHAAESSVAQDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPI 426
           L     G +LD   E+   +   ++L ++   + +A    SGGNQQKV++A+   R   +
Sbjct: 378 LAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQV 437

Query: 427 MLFDEPTRGIDIGAKSDIYRLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADT 486
             FDEPT G+D+G +  IY    +L   G G+L++SSDL E++ + +R  V   GR+   
Sbjct: 438 FAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAE 497

Query: 487 FSRDDWSQERILAAAF 502
            + D+ ++E++L+  F
Sbjct: 498 LAGDEITEEKVLSHFF 513


Lambda     K      H
   0.320    0.137    0.390 

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: 645
Number of extensions: 37
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: 522
Length of database: 518
Length adjustment: 35
Effective length of query: 487
Effective length of database: 483
Effective search space:   235221
Effective search space used:   235221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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