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_084932744.1 HA51_RS05190 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_002095475.1:WP_084932744.1
          Length = 502

 Score =  382 bits (981), Expect = e-110
 Identities = 218/505 (43%), Positives = 312/505 (61%), Gaps = 15/505 (2%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           PLL L+ I K+FPGV+AL    L  Y G V AL+GENGAGKST+MK+L+G Y+ D G   
Sbjct: 3   PLLQLKGIEKSFPGVKALNGASLAVYPGRVMALVGENGAGKSTMMKVLTGIYSMDAGSLQ 62

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRA 130
            + G+ V   GP+++++ G+ +I+QEL+L P L+VAENI+LGR    R G +    M   
Sbjct: 63  WL-GKDVAFSGPKASQEAGIGIIHQELNLIPQLTVAENIFLGREFVNRFGRIEWNRMYAE 121

Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
               L RL   F+    V  LSI  +Q+VEIA+ + FE+++++MDEPT  L+  ET  LF
Sbjct: 122 ADALLHRLNLRFNSHKLVGDLSIGDQQMVEIAKVLSFESQVIIMDEPTDALTDTETLSLF 181

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
            +I +L+ +G  I+YISHRM EI E+ D VTV RDG F+     + LS+ +L++MMVGR 
Sbjct: 182 RVINELKAQGCGIVYISHRMKEIFEICDDVTVFRDGQFIAERAVSDLSEESLIEMMVGRK 241

Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310
           L   Y   H      ++ L+V  ++ G  V   SF+LR GE+LG++GL+GAGRTEL +++
Sbjct: 242 LEDQYP--HIDQAPGDIRLTVEHLS-GPGVDNVSFNLRKGEILGISGLMGAGRTELMKVL 298

Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370
           +GA  R++G V +           +    P+  +  GI Y++EDRK  GL L  SV EN+
Sbjct: 299 YGALPRSKGTVTLNGRE-------IMTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENM 351

Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430
           +L      +   G L  +  +    + I    ++    +  +G LSGGNQQKV ++R L 
Sbjct: 352 SLTALRYFSHATGNLKHSEEQLAVGDFIRLFNVKTPSMEQPIGLLSGGNQQKVAIARGLM 411

Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490
            +P VLILDEPTRGVD+GAK EIY+LIN     G++I+++SSE+PEV+G+ DR+LVM EG
Sbjct: 412 TRPNVLILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEG 471

Query: 491 TLAGEVRPAGSAAETQERIIALATG 515
            L+GE         TQE ++A A G
Sbjct: 472 HLSGEF---SREQATQESLMAAAVG 493



 Score = 84.3 bits (207), Expect = 1e-20
 Identities = 66/242 (27%), Positives = 106/242 (43%), Gaps = 23/242 (9%)

Query: 24  PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83
           PGV     V      GE+  + G  GAG++ LMK+L GA     G    ++G+ +    P
Sbjct: 266 PGVD---NVSFNLRKGEILGISGLMGAGRTELMKVLYGALPRSKG-TVTLNGREIMTRSP 321

Query: 84  QSARDLGVAVIYQELS---LAPNLSVAENIYL----------GRALQRRGLVARGDMVRA 130
           Q     G+  I ++     L   +SV EN+ L          G        +A GD +R 
Sbjct: 322 QDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSHATGNLKHSEEQLAVGDFIRL 381

Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
                       S    +  LS   +Q V IAR +     +L++DEPT  +       ++
Sbjct: 382 FNVKTP------SMEQPIGLLSGGNQQKVAIARGLMTRPNVLILDEPTRGVDVGAKKEIY 435

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
            LI Q + EG++I+ +S  M E+  ++DR+ V+ +G   G   R   +Q +L+   VG+ 
Sbjct: 436 QLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSREQATQESLMAAAVGKQ 495

Query: 251 LS 252
            S
Sbjct: 496 HS 497


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: 578
Number of extensions: 28
Number of successful extensions: 8
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: 502
Length adjustment: 35
Effective length of query: 505
Effective length of database: 467
Effective search space:   235835
Effective search space used:   235835
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:

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:

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:

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:

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