GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas fluorescens GW456-L13

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          Length = 514

 Score =  348 bits (893), Expect = e-100
 Identities = 213/486 (43%), Positives = 288/486 (59%), Gaps = 15/486 (3%)

Query: 14  LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 73
           L    I KTFPGV+AL  +   A+ G+VHALMGENGAGKSTL+KIL GAYT   G    I
Sbjct: 16  LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGA-LQI 74

Query: 74  DGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAP 133
             + +       +   GVAVI+QEL L P ++VAEN++LG      GL+ R  + +    
Sbjct: 75  GERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALA 134

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

Query: 194 RQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL-DRAHLSQAALVKMMVGRDLS 252
            +LR EG  +LY+SHRM E+  + + VTV +DG +V T  D + L+   LV  MVGRD+ 
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQ 254

Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312
             Y     Q     V L V  +      +  SF++  GE+LGL GLVGAGRTEL RL+ G
Sbjct: 255 DIYDYRPRQ--RGAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSG 312

Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372
               + G++++           L    PR AI AGI    EDRK +G+    SV ENIN 
Sbjct: 313 LARHSAGQLKLRGH-------ELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENIN- 364

Query: 373 IVAARDALG-LGRLNRTAARRRTTE-AIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430
            ++AR A    G L R    +   E  I  L ++  +A   +  LSGGNQQK +L R L 
Sbjct: 365 -ISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLS 423

Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490
           +  +VL+LDEPTRG+DIGAK+EIY++I+ LA  G+A++++SS+L EV+G+ DR+LV+ EG
Sbjct: 424 MPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEG 483

Query: 491 TLAGEV 496
            L GE+
Sbjct: 484 ALRGEL 489



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 60/233 (25%), Positives = 113/233 (48%), Gaps = 10/233 (4%)

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

Query: 84  QSARDLGVAVIYQELS---LAPNLSVAENIYLGR--ALQRRGLVARGDMVRACAPTLARL 138
           + A   G+ +  ++     + P  SVAENI +    A    G + RG   +  A    + 
Sbjct: 334 RDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAEQQIKA 393

Query: 139 GADFSP--AANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196
               +P  A  +  LS   +Q   + R +    ++L++DEPT  +       ++ +I  L
Sbjct: 394 LKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453

Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249
             EG+A++ +S  + E+  ++DR+ VL +G   G L R   +++ L+++ + R
Sbjct: 454 AAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQLALPR 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: 613
Number of extensions: 30
Number of successful extensions: 9
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:

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