GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TAT in Pseudomonas fluorescens FW300-N2E3

Align tryptophan permease (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter

Query= CharProtDB::CH_091156
         (592 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05965 AO353_05965 aromatic
           amino acid transporter
          Length = 466

 Score =  204 bits (520), Expect = 5e-57
 Identities = 131/394 (33%), Positives = 207/394 (52%), Gaps = 10/394 (2%)

Query: 78  LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137
           LKR LK RH+ +IA+GG+IGTGLF+GS   +   GP  +++G+AIAG      +  LGE+
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAIAGFIAFLIMRQLGEM 69

Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197
            V  PV G+F+++   +      F+    Y + +  V   E+ A    VQ+W   +   +
Sbjct: 70  IVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWV 129

Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIIL-CVVLICG-GGPDHEFIGA 255
             A+F+ ++  IN   V+ FGE EF F+ IK + + G I L C +L+ G GGP      +
Sbjct: 130 SAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGPQASV--S 187

Query: 256 KYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETDP--KGLPSAIKQVFWRILF 313
             W   G   NG  G+L  +    +S GG+E+  + + E     K +P AI QV +R+L 
Sbjct: 188 NLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRVLI 247

Query: 314 FFLISLTLVGFLVPYTN--QNL-LGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLS 370
           F++ +LT++  L P+    Q L   G +   SPFV    L        I+N V+L + LS
Sbjct: 248 FYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVLTAALS 307

Query: 371 VGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEV 430
           V NS ++ +SR L  +A QG  P     +++ G PL  +  ++L  +L  +V   + +E 
Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYVAPNEA 367

Query: 431 FNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQG 464
              L A+   +  I W  I+L+H++FR AM  +G
Sbjct: 368 LELLFALVVASLMINWAMISLTHLKFRKAMGQRG 401


Lambda     K      H
   0.326    0.141    0.447 

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: 721
Number of extensions: 42
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: 592
Length of database: 466
Length adjustment: 35
Effective length of query: 557
Effective length of database: 431
Effective search space:   240067
Effective search space used:   240067
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 (21.6 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 (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