Alignments for a candidate for rbsA in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pantoea rwandensis LMG 26275

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_084935592.1 HA51_RS15895 sugar ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_002095475.1:WP_084935592.1
          Length = 501

 Score =  419 bits (1077), Expect = e-121
 Identities = 222/498 (44%), Positives = 336/498 (67%), Gaps = 10/498 (2%)

Query: 12  LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71
           +LE R IT+ F    A+  V L ++ GEV AL+GENGAGKSTLMKILAG Y    G+I +
Sbjct: 6   ILEMREITRRFGSFYALKGVDLTVWPGEVHALMGENGAGKSTLMKILAGAYTASSGEILI 65

Query: 72  EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131
           +G+    + P+EA   GI LI QE++L PNL+ AENIFL  E +   G+++ ++M E+A 
Sbjct: 66  DGQPYAIKGPKEALAAGITLIYQEINLAPNLTVAENIFLGSE-ITRGGLVKRRQMAEEAQ 124

Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191
            + ++LG        V  LS ++QQ V IA+AL  +++I++MDEPT+A+  RETEQLF +
Sbjct: 125 LVINRLGAQFSATDLVSRLSIAEQQQVEIARALHRNSRILVMDEPTAALSNRETEQLFAL 184

Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSID 251
           I+ L++EG ++IYISHR+ E++E++DRV V+RDG+ VG    ++ +  +LVR+MVGR + 
Sbjct: 185 IKRLRSEGMAIIYISHRMAEVYELSDRVSVLRDGQYVGSLTRDQLNASELVRMMVGRPLS 244

Query: 252 QFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELLE 311
             F K+R     EI R+    L   D +K  V   S  VR GE++G+ GLVGAGR+EL +
Sbjct: 245 DLFNKDRNIPFGEI-RLAVNHL--TDNRK--VHPSSLAVRAGEIVGLAGLVGAGRSELAQ 299

Query: 312 AIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLPS 371
            IFG H  +  G+++I G+++KIHSPRDA+  GIG + E+RK  GL L+++   NI + +
Sbjct: 300 LIFGVHQPKG-GEIWIDGEKVKIHSPRDAIARGIGFLTENRKEQGLFLELAAQENIVMAT 358

Query: 372 VVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIK 431
           +        +GL++ +  ++I    IE LNI+ P        LSGGNQQK+++++W++I 
Sbjct: 359 IERDA---SYGLLNRRKGQKIASEAIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSIA 415

Query: 432 PKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRK 491
           P++LLLDEPTRG+DV AKSEIY+++++MA  G+ ++M+SSELPE++ MSDR+ VM EG  
Sbjct: 416 PRILLLDEPTRGVDVGAKSEIYRMMNQMAQQGVAILMISSELPEVVGMSDRVYVMREGSI 475

Query: 492 TAEFLREEVTEEDLLKAA 509
             E   +E+++E+++  A
Sbjct: 476 AGELSGKEISQENIMTLA 493



 Score =  107 bits (266), Expect = 1e-27
 Identities = 65/236 (27%), Positives = 128/236 (54%), Gaps = 14/236 (5%)

Query: 26  IAVNNVT---------LQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEV 76
           +AVN++T         L +  GE+  L G  GAG+S L +++ GV+    G+I+++G++V
Sbjct: 260 LAVNHLTDNRKVHPSSLAVRAGEIVGLAGLVGAGRSELAQLIFGVHQPKGGEIWIDGEKV 319

Query: 77  RFRNPREAQENGIALIPQ---ELDLVPNLSSAENIFLSR-EPVNEFGVIEYQKMFEQASK 132
           +  +PR+A   GI  + +   E  L   L++ ENI ++  E    +G++  +K  + AS+
Sbjct: 320 KIHSPRDAIARGIGFLTENRKEQGLFLELAAQENIVMATIERDASYGLLNRRKGQKIASE 379

Query: 133 LFSKLGVNID-PKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191
               L + +   + +   LS   QQ + I++ +S+  +I+++DEPT  +      +++ +
Sbjct: 380 AIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSIAPRILLLDEPTRGVDVGAKSEIYRM 439

Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVG 247
           +  +  +G +++ IS  L E+  ++DRV VMR+G   GE   +E   + ++ L  G
Sbjct: 440 MNQMAQQGVAILMISSELPEVVGMSDRVYVMREGSIAGELSGKEISQENIMTLATG 495



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 60/227 (26%), Positives = 116/227 (51%), Gaps = 10/227 (4%)

Query: 286 VSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGI 345
           V   V  GEV  + G  GAG++ L++ + GA+   + G++ I G+   I  P++A+  GI
Sbjct: 25  VDLTVWPGEVHALMGENGAGKSTLMKILAGAYTA-SSGEILIDGQPYAIKGPKEALAAGI 83

Query: 346 GLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTP 405
            L+ ++     L   ++V  NI L S + +      GL+  +   E  +  I +L  +  
Sbjct: 84  TLIYQE---INLAPNLTVAENIFLGSEITR-----GGLVKRRQMAEEAQLVINRLGAQF- 134

Query: 406 SPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMG 465
           S   +V  LS   QQ+V +A+ L    ++L++DEPT  +      +++ LI  +   GM 
Sbjct: 135 SATDLVSRLSIAEQQQVEIARALHRNSRILVMDEPTAALSNRETEQLFALIKRLRSEGMA 194

Query: 466 VVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPR 512
           ++ +S  + E+  +SDR+ V+ +G+      R+++   +L++  + R
Sbjct: 195 IIYISHRMAEVYELSDRVSVLRDGQYVGSLTRDQLNASELVRMMVGR 241


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: 616
Number of extensions: 21
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 523
Length of database: 501
Length adjustment: 35
Effective length of query: 488
Effective length of database: 466
Effective search space:   227408
Effective search space used:   227408
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 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:

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 2024 update 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