GapMind for catabolism of small carbon sources

 

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

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3653 N515DRAFT_3653 amino
           acid/polyamine/organocation transporter, APC superfamily
           (TC 2.A.3)
          Length = 453

 Score =  408 bits (1049), Expect = e-118
 Identities = 197/438 (44%), Positives = 288/438 (65%), Gaps = 6/438 (1%)

Query: 9   EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68
           + L+R L  RHI  +ALG AIG GLFLGSA+ I  AGP ++  Y   G + F+IMR LGE
Sbjct: 3   QHLQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGE 62

Query: 69  MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128
           M V +PVAGSFS +A++Y G FAG+ +GWNYW+L V V MAE TAVG Y++ W+PE+P W
Sbjct: 63  MAVHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQW 122

Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG--NGGPQATV 186
           +       +I  +NL  VKV+GEMEFWF +IKV+ VV MI+ G  +++ G  NGG    +
Sbjct: 123 IWVFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGL 182

Query: 187 SNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRIL 246
           +NLW  GG+ PHGFTG+V+ + +++F+FGG+E +G+ A EA  PE++IP+A N V++RIL
Sbjct: 183 ANLWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRIL 242

Query: 247 IFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYC 306
           IFY+G+L V++++ PW ++    SPFV  F +LG    A  +N VV+TAALS +NS  + 
Sbjct: 243 IFYVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFS 302

Query: 307 NSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALV 366
            SRML+ L+ +  AP  L  V + GVPV  +LV+       V++NYL PE  F ++M+++
Sbjct: 303 GSRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSIL 362

Query: 367 VSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTPGM 426
               V  W M+ +AH  FRR    +   T FP   +PL + +CLLF+A VL ++  +   
Sbjct: 363 AFNTVWTWMMVLIAHYSFRR----RHGATAFPLRAWPLTSVVCLLFLAFVLFMLGYSADT 418

Query: 427 AISVYLIPVWLIVLGIGY 444
            +++Y+   W+++L + Y
Sbjct: 419 RVALYVGAGWVVLLSLAY 436


Lambda     K      H
   0.328    0.141    0.434 

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: 709
Number of extensions: 46
Number of successful extensions: 3
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: 457
Length of database: 453
Length adjustment: 33
Effective length of query: 424
Effective length of database: 420
Effective search space:   178080
Effective search space used:   178080
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 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