GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens GW456-L13

Align L-tyrosine transporter (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP

Query= reanno::pseudo5_N2C3_1:AO356_18530
         (471 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Aromatic
           amino acid transport protein AroP
          Length = 467

 Score =  705 bits (1819), Expect = 0.0
 Identities = 338/453 (74%), Positives = 397/453 (87%)

Query: 1   MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60
           M+ +    GELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAI GFIAF
Sbjct: 1   MADEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAF 60

Query: 61  MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120
           +IMRQLGEMIVEEPVAGSFSHFAHKYWGG+AGFLSGWN W+LY+LVGM+ELTAVGKY+ +
Sbjct: 61  LIMRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQF 120

Query: 121 WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180
           W P++P+WVSAA FF+L+N IN+ NVKVFGE EFWFAIIKVVAI+GMIALG Y+L SG G
Sbjct: 121 WWPEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTG 180

Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240
           GPQASV+NLW HGGFFPNG SGL+MAMA IMFSFGGLE++G TAAEA +P  VIPKAINQ
Sbjct: 181 GPQASVSNLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAINQ 240

Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300
           V+YR+LIFY+GAL VLLSL PWD LL TL ASGDAY GSPFVQ+FS++GS+TAAHILNFV
Sbjct: 241 VVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILNFV 300

Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360
           VLTAALSVYNSG YCNSRML G+AEQGDAPKAL +++K+GVP+ ++  SA +TL++VL+N
Sbjct: 301 VLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVLVN 360

Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA 420
           YL P  ALELL +LVVA+L+INWAMIS +H KFR+ M+Q    P FK+ W+P+ NY+CLA
Sbjct: 361 YLAPHEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGIVPGFKSFWFPFSNYLCLA 420

Query: 421 FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCY 453
           F+V I+ VML+IPGI+ SV+AIPVWV+ ++  Y
Sbjct: 421 FMVMIVCVMLMIPGIRASVFAIPVWVLIIFGFY 453


Lambda     K      H
   0.327    0.139    0.432 

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: 759
Number of extensions: 29
Number of successful extensions: 1
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: 471
Length of database: 467
Length adjustment: 33
Effective length of query: 438
Effective length of database: 434
Effective search space:   190092
Effective search space used:   190092
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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