GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_3653
          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 (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