GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Pseudomonas fluorescens FW300-N2C3

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20250 AO356_20250
           L-arabinose transporter ATP-binding protein
          Length = 514

 Score =  354 bits (909), Expect = e-102
 Identities = 211/485 (43%), Positives = 290/485 (59%), Gaps = 13/485 (2%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L    I K+FPGV+AL  +   A+ G+VHALMGENGAGKSTL+KIL GAY     G+  I
Sbjct: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPS-SGDLQI 74

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133
             Q +   G   +   GVAVI+QEL L P ++VAEN++LG    R GLV RG + +    
Sbjct: 75  GEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALT 134

Query: 134 TLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALI 193
            L  L  +  P   V  LS+ QRQLVEIA+A+   A ++  DEPT+ LS  E DRL A+I
Sbjct: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194

Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDR-AHLSQAALVKMMVGRDLS 252
            +LR EG  +LY+SHRM E+  + + VTV +DG +V T +  + L+   LV  MVGRD+ 
Sbjct: 195 ARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254

Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312
             Y   +      +V L V+ +      +  SF +  GE+LGL GLVGAGRTEL RL+ G
Sbjct: 255 DIY--DYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRLLSG 312

Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372
            + ++ G + +           L    PR AI AG+    EDRK +G+    SV ENIN+
Sbjct: 313 LERQSEGSLVLHGK-------ELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINI 365

Query: 373 IV-AARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431
               A  ALG   L     R    + I +L ++   A   +  LSGGNQQK +L R L +
Sbjct: 366 SARPAHSALGC-LLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSM 424

Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491
             +VL+LDEPTRG+DIGAK+EIY++I+ LA  G+A++++SS+L EV+G+ DR+LV+ EG 
Sbjct: 425 PMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGA 484

Query: 492 LAGEV 496
           + GE+
Sbjct: 485 MRGEL 489



 Score = 82.0 bits (201), Expect = 5e-20
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 10/233 (4%)

Query: 24  PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83
           PG+R    V    + GE+  L G  GAG++ L ++LSG      G    + G+ +++  P
Sbjct: 277 PGLR--EPVSFQVHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLV-LHGKELKLRSP 333

Query: 84  QSARDLGVAVIYQELS---LAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARL 138
           + A   GV +  ++     + P  SV ENI +    A    G + RGD  R  A    + 
Sbjct: 334 RDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSALGCLLRGDWERGNADKQIKS 393

Query: 139 GADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
               +PAA+  +  LS   +Q   + R +    ++L++DEPT  +       ++ +I  L
Sbjct: 394 LKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249
             +G+A++ +S  + E+  ++DR+ VL +G   G L R   +++ L+++ + R
Sbjct: 454 AADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPR 506


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: 622
Number of extensions: 29
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: 514
Length adjustment: 35
Effective length of query: 505
Effective length of database: 479
Effective search space:   241895
Effective search space used:   241895
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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