GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas fluorescens GW456-L13

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate PfGW456L13_3211 Arginine permease RocE

Query= TCDB::Q2VQZ4
         (536 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3211
          Length = 474

 Score =  247 bits (631), Expect = 6e-70
 Identities = 147/474 (31%), Positives = 238/474 (50%), Gaps = 23/474 (4%)

Query: 33  LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEM 92
           L + LK+RH+ M+++GG IG GLF+GSG  + +GGP   ++ YL+ G ++    + L E+
Sbjct: 16  LTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGFLMYLVMVCLGEL 75

Query: 93  AVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAV 152
           +V  PV+G+F T+  +++ P+ GF +GW Y ++W T +  E  AA + +  W  ++ +  
Sbjct: 76  SVQMPVSGSFQTHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIWY 135

Query: 153 WVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCG----GVGDQGYI 208
           W ++F+VVL GI     R +GE E+  S IK+ A +GFI++G+++  G      G    +
Sbjct: 136 WSALFVVVLFGINAMATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGVMPLSSGAPAPM 195

Query: 209 GVKYWRDPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIA 268
                 D           AV +   ++F G E++G+AA E+  P KSIP A + V +R+ 
Sbjct: 196 ATNLIGDSLFPNGLSAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVFRVL 255

Query: 269 IFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLS 328
           IFY+L + ++  I+P     LM         SPFV      GI     +MN VI  A+LS
Sbjct: 256 IFYVLAIIVLSAIVPWQQAGLM--------ESPFVQVFDMVGIPYAADLMNFVILTAILS 307

Query: 329 VANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEI 388
           V NS  + STR + AM++  MAP     +  +G PL  + + + F L++ + +      +
Sbjct: 308 VGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFVAADTL 367

Query: 389 FGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLGLGLNIL 448
           F  L+A++G+     W  I LA  + R      G  L  + Y+ P+     +  L L  +
Sbjct: 368 FMVLMAVSGMSGTVTWIVIALAQYKFRKAYLRDGGKLRDLKYRAPW-----FPVLPLMCI 422

Query: 449 ALIASFYTALFPASGASPTAEAFFSSYLAFFSVTLLYLGYKACTRKRQMYVRPA 502
            L  S +  L       P      S Y  F  + L Y  Y    RKR   + P+
Sbjct: 423 TLCCSLFVFLALDETQRP------SLYWGFGFIALCYGAYFLIHRKRGAVLAPS 470


Lambda     K      H
   0.327    0.142    0.442 

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: 638
Number of extensions: 32
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 536
Length of database: 474
Length adjustment: 34
Effective length of query: 502
Effective length of database: 440
Effective search space:   220880
Effective search space used:   220880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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