GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TAT in Dyella japonica UNC79MFTsu3.2

Align tryptophan permease (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= CharProtDB::CH_091156
         (592 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2630 N515DRAFT_2630 amino
           acid/polyamine/organocation transporter, APC superfamily
          Length = 454

 Score =  184 bits (468), Expect = 5e-51
 Identities = 119/401 (29%), Positives = 200/401 (49%), Gaps = 25/401 (6%)

Query: 77  NLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGE 136
           +L+R L+ RH+ ++A+G +IG GLF+GS  AI   GP  +++ + + G  I   +  LGE
Sbjct: 6   SLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGP-AILLSYLLGGVAIFIIMRALGE 64

Query: 137 ITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPV 196
           + V+ PV G+F+ Y   +L P   ++    Y   W      EI A  + +  W   +   
Sbjct: 65  MAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQW 124

Query: 197 IWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEF-IG- 254
           IW       + ++NL  V+ +GE EF F+ IK +T+       V++I GGG    F +G 
Sbjct: 125 IWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTI-------VLMIVGGGAMIVFGLGN 177

Query: 255 -------AKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIK 305
                  +  W   G + NG  G+L  L +  ++  G+EM  L +GE D   K +P AI 
Sbjct: 178 QGVPTGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAIN 237

Query: 306 QVFWRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVIL 365
            VFWRIL F++ +L ++  + P+   N LG      SPFV+  +   IK+   I+N V+L
Sbjct: 238 SVFWRILIFYVGALFVIMSIYPW---NELG---THGSPFVMTFERLGIKSAAGIINFVVL 291

Query: 366 ISVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSG 425
            + LS  N  I+++ R L ++A QG  P  F     +G P   ++ + +  L   L+   
Sbjct: 292 TAALSSCNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYL 351

Query: 426 SMSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKS 466
             ++VF W+ + A       W  + ++ +++R  +    +S
Sbjct: 352 VPAKVFVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRS 392


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: 713
Number of extensions: 46
Number of successful extensions: 5
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: 454
Length adjustment: 35
Effective length of query: 557
Effective length of database: 419
Effective search space:   233383
Effective search space used:   233383
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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