Alignments for a candidate for rbsA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Paraburkholderia bryophila 376MFSha3.1

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  449 bits (1156), Expect = e-131
 Identities = 240/499 (48%), Positives = 336/499 (67%), Gaps = 7/499 (1%)

Query: 13  LEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVY-PDYEGQIFL 71
           LE RNI++TFPGV A++ V L+I  GEV AL GENGAGKSTLMKIL G+Y PD  G I +
Sbjct: 10  LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131
           EG+EV   +   A+  G+ +I QEL +V NL+  ENIFL+REP    G+I+  +M+ +A 
Sbjct: 70  EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129

Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191
           ++ + + ++IDP T+V +LS  QQQM+ IAKAL   +K IIMDEPT+++   ET  L  I
Sbjct: 130 EVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGI 189

Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSID 251
           ++ L+    +V+YISHRLEEIFE+ADRV V+RDGR VG  PI +   + LVRLMV R + 
Sbjct: 190 VKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVARELS 249

Query: 252 QFFIKERATIT-DEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELL 310
           + + + ++  + D +  V  + L  + + +  + D+SF + +GEVLGI GLVG+GRTE++
Sbjct: 250 ELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGRTEIM 309

Query: 311 EAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLP 370
           E IFG       G V I GK + I +P DA+++GIG V EDRK  GLIL M+V  N +L 
Sbjct: 310 EMIFGMR--ACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSLT 367

Query: 371 SVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAI 430
            +        F  +    E+E  R F+  L IKTP   Q V NLSGGNQQK+V+AKW+A 
Sbjct: 368 HLER---YSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVAR 424

Query: 431 KPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGR 490
            PKVL++DEPTRGIDV AK+E++ LI+ +A  G+GV+++SS+L E+LA+SDRIL + EGR
Sbjct: 425 SPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGR 484

Query: 491 KTAEFLREEVTEEDLLKAA 509
            + E  R + ++E ++  A
Sbjct: 485 ISGELSRAQASQEKVMALA 503



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 59/232 (25%), Positives = 111/232 (47%), Gaps = 8/232 (3%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342
           +D V+  +R GEVL + G  GAG++ L++ + G +     G + + G+E+ +     A  
Sbjct: 25  LDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILVEGQEVALADSHHART 84

Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402
            G+ ++ ++    G    ++V  NI L          + GLID        R  +  +++
Sbjct: 85  LGVNIIYQELAVVG---NLTVGENIFLAREPRT----RLGLIDRPRMYREAREVLATIDM 137

Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462
               P   V  LS G QQ + +AK L  + K +++DEPT  +  +  S +  ++  +   
Sbjct: 138 DI-DPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGIVKRLRER 196

Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514
            + VV +S  L EI  ++DR+ V+ +GR        ++T E L++  + R +
Sbjct: 197 NIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVAREL 248


Lambda     K      H
   0.317    0.137    0.372 

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: 625
Number of extensions: 22
Number of successful extensions: 10
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: 523
Length of database: 505
Length adjustment: 35
Effective length of query: 488
Effective length of database: 470
Effective search space:   229360
Effective search space used:   229360
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 (21.6 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, or view the source code.

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