GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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