GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N1B4

Align L-tyrosine transporter (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559
          Length = 473

 Score =  902 bits (2332), Expect = 0.0
 Identities = 450/470 (95%), Positives = 459/470 (97%)

Query: 1   MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60
           MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF
Sbjct: 1   MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60

Query: 61  MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120
           MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY
Sbjct: 61  MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120

Query: 121 WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180
           WAPDIPTWVSAA FF+LIN INLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSG G
Sbjct: 121 WAPDIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDG 180

Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240
           GPQASVTNLW HGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ
Sbjct: 181 GPQASVTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240

Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300
           VIYRILIFYIGALVVLLSLTPWDSLL TLNASGDAYSGSPFVQVFSMLGS+TAAHILNFV
Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFV 300

Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360
           VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALS+IDKRGVPVRSILASAAVTLVAVLLN
Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLN 360

Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA 420
           YLVPQHALELLMSLVVATLVINWAMIS+SHFKFRQHMN+T+QTPLFKALWYPYGNY+CLA
Sbjct: 361 YLVPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPLFKALWYPYGNYVCLA 420

Query: 421 FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELAVAAA 470
           FVVFILGVMLLIPGIQISVYAIPVWV FMWVCY IKNKRSA+Q L  A +
Sbjct: 421 FVVFILGVMLLIPGIQISVYAIPVWVAFMWVCYGIKNKRSAQQALQAAGS 470


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: 899
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: 473
Length adjustment: 33
Effective length of query: 438
Effective length of database: 440
Effective search space:   192720
Effective search space used:   192720
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:

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