GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_05965
          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:

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