Alignments for a candidate for frcA in Pantoea rwandensis LMG 26275

GapMind for catabolism of small carbon sources

Alignments for a candidate for frcA in Pantoea rwandensis LMG 26275

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_084935592.1 HA51_RS15895 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_002095475.1:WP_084935592.1
          Length = 501

 Score =  507 bits (1305), Expect = e-148
 Identities = 285/505 (56%), Positives = 359/505 (71%), Gaps = 13/505 (2%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P+L +R I + F    AL+ V+LT + GEVHALMGENGAGKSTLMKIL+GAYTA   GE 
Sbjct: 5   PILEMREITRRFGSFYALKGVDLTVWPGEVHALMGENGAGKSTLMKILAGAYTAS-SGEI 63

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
            IDGQ   I GP+ A   G+ +IYQE++LAPNL+VAENI+LG  + R GLV R  M    
Sbjct: 64  LIDGQPYAIKGPKEALAAGITLIYQEINLAPNLTVAENIFLGSEITRGGLVKRRQMAEEA 123

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              + RLGA FS    V+ LSIA++Q VEIARA+H  +RILVMDEPT  LS  ET++LFA
Sbjct: 124 QLVINRLGAQFSATDLVSRLSIAEQQQVEIARALHRNSRILVMDEPTAALSNRETEQLFA 183

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           LI++LR EGMAI+YISHRMAE+ EL+DRV+VLRDG +VG+L R  L+ + LV+MMVGR L
Sbjct: 184 LIKRLRSEGMAIIYISHRMAEVYELSDRVSVLRDGQYVGSLTRDQLNASELVRMMVGRPL 243

Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311
           S  + K        E+ L+V  + D R+V   S  +RAGE++GLAGLVGAGR+ELA+L+F
Sbjct: 244 SDLFNKDRNIPF-GEIRLAVNHLTDNRKVHPSSLAVRAGEIVGLAGLVGAGRSELAQLIF 302

Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371
           G      GE+ I      G  V + +  PR AI  GI +LTE+RK QGLFL+ +  ENI 
Sbjct: 303 GVHQPKGGEIWI-----DGEKVKIHS--PRDAIARGIGFLTENRKEQGLFLELAAQENIV 355

Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431
           +    RDA   G LNR   ++  +EAI++L IRV HAQV  G LSGGNQQK+++SR + I
Sbjct: 356 MATIERDA-SYGLLNRRKGQKIASEAIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSI 414

Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491
            PR+L+LDEPTRGVD+GAKSEIYR++N +AQ GVAILMISSELPEVVG+ DRV VMREG+
Sbjct: 415 APRILLLDEPTRGVDVGAKSEIYRMMNQMAQQGVAILMISSELPEVVGMSDRVYVMREGS 474

Query: 492 LAGEVRPAGSAAETQERIIALATGA 516
           +AGE+        +QE I+ LATGA
Sbjct: 475 IAGEL---SGKEISQENIMTLATGA 496



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 72/255 (28%), Positives = 121/255 (47%), Gaps = 9/255 (3%)

Query: 1   MSDMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILS 60
           +SD+ +     P   +R         R +    L   AGE+  L G  GAG+S L +++ 
Sbjct: 243 LSDLFNKDRNIPFGEIRLAVNHLTDNRKVHPSSLAVRAGEIVGLAGLVGAGRSELAQLIF 302

Query: 61  GAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQ---ELSLAPNLSVAENIYLGRALQ 117
           G +    GGE  IDG++V+I  P+ A   G+  + +   E  L   L+  ENI +   ++
Sbjct: 303 GVH-QPKGGEIWIDGEKVKIHSPRDAIARGIGFLTENRKEQGLFLELAAQENIVMA-TIE 360

Query: 118 R---RGLVARGDMVRACAPTLARLGADFSPA-ANVASLSIAQRQLVEIARAVHFEARILV 173
           R    GL+ R    +  +  +  L      A      LS   +Q + I+R V    RIL+
Sbjct: 361 RDASYGLLNRRKGQKIASEAIESLNIRVPHAQVRAGGLSGGNQQKLLISRWVSIAPRILL 420

Query: 174 MDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD 233
           +DEPT  +       ++ ++ Q+  +G+AIL IS  + E+  ++DRV V+R+G   G L 
Sbjct: 421 LDEPTRGVDVGAKSEIYRMMNQMAQQGVAILMISSELPEVVGMSDRVYVMREGSIAGELS 480

Query: 234 RAHLSQAALVKMMVG 248
              +SQ  ++ +  G
Sbjct: 481 GKEISQENIMTLATG 495


Lambda     K      H
   0.320    0.136    0.382 

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: 658
Number of extensions: 26
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: 540
Length of database: 501
Length adjustment: 35
Effective length of query: 505
Effective length of database: 466
Effective search space:   235330
Effective search space used:   235330
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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