GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Pseudomonas fluorescens FW300-N1B4

Align Amino-acid permease GAP1 (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP

Query= SwissProt::Q5AG77
         (582 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Aromatic amino acid
           transport protein AroP
          Length = 473

 Score =  244 bits (623), Expect = 6e-69
 Identities = 151/443 (34%), Positives = 237/443 (53%), Gaps = 11/443 (2%)

Query: 65  NAANSNLQRKLKTRHLQMIAIGSSIGTGLFVGTGGALSTGGPAAIVLAWAISAISVFMTM 124
           N+ +  L+R LK RH+Q+IA+G +IGTGLF+G+ G L + GP+ ++L +AI     FM M
Sbjct: 5   NSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAICGFIAFMIM 63

Query: 125 QGLGELAVAFPVSGGFNLYASKFLEPGIGFAVGWNYFLQFFVLLPLELVAGAITIKYWNA 184
           + LGE+ V  PV+G F+ +A K+     GF  GWN ++ + ++   EL A    I YW  
Sbjct: 64  RQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP 123

Query: 185 SINSDVFVIIFWFVVLVITMLGVRWYGEAELVFCTIKVIAVIGFIILGIVLICGGGPNHE 244
            I + V    F+ ++ +I +  V+ +GEAE  F  IKV+A++G I LG  L+  G    +
Sbjct: 124 DIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDGGPQ 183

Query: 245 FIGGKYWREPGPFANSFKGFASSLITAAFSFGGTEMIALTASESSNVRHALPKAIKQVFW 304
                 W   G F N   G   ++    FSFGG EM+  TA+E+   +  +PKAI QV +
Sbjct: 184 ASVTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIY 243

Query: 305 RIVIFYLGSIIMIATLVPYND-KRLLGSSSVDVTASPFTIAIVNGGIKGLPSVINAVILI 363
           RI+IFY+G+++++ +L P++     L +S    + SPF       G      ++N V+L 
Sbjct: 244 RILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLT 303

Query: 364 SVLSVGNASVYATSRTLNSLAEQGMAPKWTGYIDRAGRPLFAILITNVFGLFALIAADNE 423
           + LSV N+  Y  SR L  +AEQG APK    ID+ G P+ +IL +    L A++     
Sbjct: 304 AALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLNYLV 363

Query: 424 KQVVAFNWLLALSGLSSIFTWMSINLSHIRFRRAMKVQNRSLTELPFVAQSGVWGSYFGL 483
            Q  A   L++L   + +  W  I+ SH +FR+ M   N++     F A    +G+Y  L
Sbjct: 364 PQ-HALELLMSLVVATLVINWAMISFSHFKFRQHM---NKTKQTPLFKALWYPYGNYVCL 419

Query: 484 T-----LNILYLIAQFYIGLFPV 501
                 L ++ LI    I ++ +
Sbjct: 420 AFVVFILGVMLLIPGIQISVYAI 442


Lambda     K      H
   0.325    0.140    0.430 

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: 701
Number of extensions: 40
Number of successful extensions: 4
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: 582
Length of database: 473
Length adjustment: 35
Effective length of query: 547
Effective length of database: 438
Effective search space:   239586
Effective search space used:   239586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 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, 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