Alignments for a candidate for ytfR in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Pantoea rwandensis LMG 26275

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_084935592.1 HA51_RS15895 sugar ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_002095475.1:WP_084935592.1
          Length = 501

 Score =  368 bits (944), Expect = e-106
 Identities = 200/487 (41%), Positives = 302/487 (62%), Gaps = 2/487 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           IL    +++ F    AL  VD ++  GE+ AL+GENGAGKSTL+K L G Y A  G I +
Sbjct: 6   ILEMREITRRFGSFYALKGVDLTVWPGEVHALMGENGAGKSTLMKILAGAYTASSGEILI 65

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +GQ  + K    A   GI  +YQE+NL PN++VA+N+F+G E  R GL++R++M + A  
Sbjct: 66  DGQPYAIKGPKEALAAGITLIYQEINLAPNLTVAENIFLGSEITRGGLVKRRQMAEEAQL 125

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           ++   G      + ++R S+A QQ V I RA+  ++++L++DEPTA+L  +E E LF L+
Sbjct: 126 VINRLGAQFSATDLVSRLSIAEQQQVEIARALHRNSRILVMDEPTAALSNRETEQLFALI 185

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
           ++LR  G+++I+++H + +VY++SDR++VLR+G +VG     +L   ELV+MM+GR L  
Sbjct: 186 KRLRSEGMAIIYISHRMAEVYELSDRVSVLRDGQYVGSLTRDQLNASELVRMMVGRPLSD 245

Query: 249 HALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFG 308
             L    R +   +   A  +      + P  L VR GEIVGLAGL+G+GR+E A++IFG
Sbjct: 246 --LFNKDRNIPFGEIRLAVNHLTDNRKVHPSSLAVRAGEIVGLAGLVGAGRSELAQLIFG 303

Query: 309 IKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRG 368
           +     G   I G+   + SP  A   GIGF  E+RK  G+    + +ENI++A   +  
Sbjct: 304 VHQPKGGEIWIDGEKVKIHSPRDAIARGIGFLTENRKEQGLFLELAAQENIVMATIERDA 363

Query: 369 WLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDE 428
               ++R++ Q+IA   I  L IR P  +     LSGGNQQK+L+SRW+   P+ L+LDE
Sbjct: 364 SYGLLNRRKGQKIASEAIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSIAPRILLLDE 423

Query: 429 PTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAE 488
           PTRG+DVGA +EI R++  +   G+A+L+ISSEL E+VG +DRV +MR+     E+   E
Sbjct: 424 PTRGVDVGAKSEIYRMMNQMAQQGVAILMISSELPEVVGMSDRVYVMREGSIAGELSGKE 483

Query: 489 LSVPAIM 495
           +S   IM
Sbjct: 484 ISQENIM 490



 Score = 99.8 bits (247), Expect = 2e-25
 Identities = 64/225 (28%), Positives = 118/225 (52%), Gaps = 14/225 (6%)

Query: 31  SLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIGTVY 90
           ++R GEI+ L G  GAG+S L + + GV+    G IW++G+ +   +   A   GIG + 
Sbjct: 277 AVRAGEIVGLAGLVGAGRSELAQLIFGVHQPKGGEIWIDGEKVKIHSPRDAIARGIGFLT 336

Query: 91  Q---EVNLLPNMSVADNLFIG--REPKRFGLLRRKEMEKRATELMASYGFSLDVREP--- 142
           +   E  L   ++  +N+ +        +GLL R++ +K A+E + S    L++R P   
Sbjct: 337 ENRKEQGLFLELAAQENIVMATIERDASYGLLNRRKGQKIASEAIES----LNIRVPHAQ 392

Query: 143 --LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIF 200
                 S   QQ + I R + ++ ++L+LDEPT  +D      ++ +M Q+  +GV+++ 
Sbjct: 393 VRAGGLSGGNQQKLLISRWVSIAPRILLLDEPTRGVDVGAKSEIYRMMNQMAQQGVAILM 452

Query: 201 VTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE 245
           ++  L +V  +SDR+ V+R GS  G     E+ Q  ++ +  G +
Sbjct: 453 ISSELPEVVGMSDRVYVMREGSIAGELSGKEISQENIMTLATGAQ 497


Lambda     K      H
   0.321    0.138    0.391 

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: 561
Number of extensions: 28
Number of successful extensions: 6
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: 500
Length of database: 501
Length adjustment: 34
Effective length of query: 466
Effective length of database: 467
Effective search space:   217622
Effective search space used:   217622
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