Alignments for a candidate for araVsh in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Pantoea rwandensis LMG 26275

Align ABC transporter related (characterized, see rationale)
to candidate WP_084935592.1 HA51_RS15895 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_002095475.1:WP_084935592.1
          Length = 501

 Score =  378 bits (970), Expect = e-109
 Identities = 195/490 (39%), Positives = 320/490 (65%), Gaps = 5/490 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           ILE+++I++ +    AL+ V L ++ GEVHAL+GENGAGKSTL+K++ GA +   G+IL 
Sbjct: 6   ILEMREITRRFGSFYALKGVDLTVWPGEVHALMGENGAGKSTLMKILAGAYTASSGEILI 65

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+P     P +A  AGI+ +YQE+NL PNLTVA+N+FLG E  R GL+  ++M  +A+ 
Sbjct: 66  DGQPYAIKGPKEALAAGITLIYQEINLAPNLTVAENIFLGSEITRGGLVKRRQMAEEAQL 125

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           V+ +       +  +S  SIA QQ + IAR +  ++++LV+DEPTA+L  +E + LF ++
Sbjct: 126 VINRLGAQFSATDLVSRLSIAEQQQVEIARALHRNSRILVMDEPTAALSNRETEQLFALI 185

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            +L+++G+AI++I+H + +VY++SDR++VLR+GQ++G     +L   +L+  M+GR L  
Sbjct: 186 KRLRSEGMAIIYISHRMAEVYELSDRVSVLRDGQYVGSLTRDQLNASELVRMMVGRPLS- 244

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
              D   K+R +   E + L++  ++    +   +L V  G+ VGLAGL+G+GRSE+   
Sbjct: 245 ---DLFNKDRNIPFGE-IRLAVNHLTDNRKVHPSSLAVRAGEIVGLAGLVGAGRSELAQL 300

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363
           +FG+     G I + G+K+ +  P DAI+ GI    E+RK  G+   L+ +ENI++A   
Sbjct: 301 IFGVHQPKGGEIWIDGEKVKIHSPRDAIARGIGFLTENRKEQGLFLELAAQENIVMATIE 360

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
           R   +  L+  + Q+IA   I+ L I  P A      LSGGNQQK++++RW++I P +L+
Sbjct: 361 RDASYGLLNRRKGQKIASEAIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSIAPRILL 420

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483
           LDEPTRG+D+GA +EI +++  +  +G+++L+ SSEL E+V  S++V V+R+     ELS
Sbjct: 421 LDEPTRGVDVGAKSEIYRMMNQMAQQGVAILMISSELPEVVGMSDRVYVMREGSIAGELS 480

Query: 484 GAELTSQHVM 493
           G E++ +++M
Sbjct: 481 GKEISQENIM 490



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 66/239 (27%), Positives = 114/239 (47%), Gaps = 6/239 (2%)

Query: 6   ELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLG 65
           E++    H    + +   SL + AGE+  L G  GAG+S L +++ G      G+I   G
Sbjct: 257 EIRLAVNHLTDNRKVHPSSLAVRAGEIVGLAGLVGAGRSELAQLIFGVHQPKGGEIWIDG 316

Query: 66  EPQHFNTPMDAQKAGISTVYQ---EVNLVPNLTVAQNLFLGYEPR--RLGLIHFKKMYAD 120
           E    ++P DA   GI  + +   E  L   L   +N+ +    R    GL++ +K    
Sbjct: 317 EKVKIHSPRDAIARGIGFLTENRKEQGLFLELAAQENIVMATIERDASYGLLNRRKGQKI 376

Query: 121 ARAVLTQFKLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179
           A   +    + +          S   QQ + I+R V+++ ++L+LDEPT  +D      +
Sbjct: 377 ASEAIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSIAPRILLLDEPTRGVDVGAKSEI 436

Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238
           + ++NQ+  +GVAI+ I+  L +V  +SDR+ V+R G   GE    E+ Q  ++    G
Sbjct: 437 YRMMNQMAQQGVAILMISSELPEVVGMSDRVYVMREGSIAGELSGKEISQENIMTLATG 495



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 65/222 (29%), Positives = 113/222 (50%), Gaps = 6/222 (2%)

Query: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAIS 332
           +++ ++LTV  G+   L G  G+G+S +   + G     SG I + GQ   +  P +A++
Sbjct: 21  ALKGVDLTVWPGEVHALMGENGAGKSTLMKILAGAYTASSGEILIDGQPYAIKGPKEALA 80

Query: 333 AGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATP 392
           AGI L  ++  +      L++ ENI L  +   G    +   +  E AQ  I++L  A  
Sbjct: 81  AGITLIYQEINL---APNLTVAENIFLGSEITRGG--LVKRRQMAEEAQLVINRLG-AQF 134

Query: 393 DADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMS 452
            A   + +LS   QQ+V +AR L     +LV+DEPT  +      ++  LI+ L  EGM+
Sbjct: 135 SATDLVSRLSIAEQQQVEIARALHRNSRILVMDEPTAALSNRETEQLFALIKRLRSEGMA 194

Query: 453 LLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQ 494
           ++  S  + E+   S++V VLRD   V  L+  +L +  +++
Sbjct: 195 IIYISHRMAEVYELSDRVSVLRDGQYVGSLTRDQLNASELVR 236


Lambda     K      H
   0.319    0.136    0.377 

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: 581
Number of extensions: 33
Number of successful extensions: 6
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: 499
Length of database: 501
Length adjustment: 34
Effective length of query: 465
Effective length of database: 467
Effective search space:   217155
Effective search space used:   217155
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 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