GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N2E3

Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter

Query= uniprot:A0A0C4YP23
         (465 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05965
          Length = 466

 Score =  634 bits (1634), Expect = 0.0
 Identities = 310/452 (68%), Positives = 366/452 (80%), Gaps = 9/452 (1%)

Query: 13  LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72
           LKRGLKNRHIQLIALGGAIGTGLFLG A  +K AGPS++LGYA+AG IAF IMRQLGEM+
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70

Query: 73  VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132
           V+EPVAGSFSHFA+ Y GSFAGF+SGWNYWVLY+LV MAEL+AVG YVQ+WWP +PTW S
Sbjct: 71  VEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWVS 130

Query: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVSNLW 192
           A  FF+L+N IN  +VK FGEMEFWF+I+KV+AI+GMI  G Y+L SGT GPQASVSNLW
Sbjct: 131 AAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGPQASVSNLW 190

Query: 193 QHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIFYV 252
            HGGFFPNG +GL+MAMA IMFSFGGLELVGITAAEA EP K IPKA NQV+YR+LIFYV
Sbjct: 191 SHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRVLIFYV 250

Query: 253 GALGVLLSLYPWEKVVT---------GGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYN 303
           GAL VLLSLYPW++++           GSPFV IF  + S+  A +LN VVLTAALSVYN
Sbjct: 251 GALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVLTAALSVYN 310

Query: 304 SGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFEL 363
           SGVYCNSRML+GLA+QG+APK+L+K+NK+G+PL ALG+SAL T  CVV+NY  P EA EL
Sbjct: 311 SGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYVAPNEALEL 370

Query: 364 LMGLVVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMY 423
           L  LVV++L+INWAMIS+ HLKFR+     G    FK+   P TNY+CLAF+A I+YVM 
Sbjct: 371 LFALVVASLMINWAMISLTHLKFRKAMGQRGIVPGFKAFWSPYTNYLCLAFMAMIIYVML 430

Query: 424 LTPGLRISVYLIPAWLAVLGLSYRLRQKQKRA 455
           L PG+R SVY IP W+ +L + YR+R  + RA
Sbjct: 431 LIPGVRASVYAIPVWVLILFVFYRIRVARTRA 462


Lambda     K      H
   0.326    0.140    0.426 

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: 739
Number of extensions: 29
Number of successful extensions: 2
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: 465
Length of database: 466
Length adjustment: 33
Effective length of query: 432
Effective length of database: 433
Effective search space:   187056
Effective search space used:   187056
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: 51 (24.3 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 (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