GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_04042 in Cupriavidus basilensis 4G11

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate RR42_RS33780 RR42_RS33780 GABA permease

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS33780 RR42_RS33780 GABA permease
          Length = 474

 Score =  323 bits (827), Expect = 1e-92
 Identities = 174/462 (37%), Positives = 265/462 (57%), Gaps = 9/462 (1%)

Query: 6   QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65
           Q  GLK GLK RH+ +IALGG IG GLF+GS  V+++AGP+ ++ + I G++  ++MR L
Sbjct: 9   QSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLLVVLVMRML 68

Query: 66  GEMVAQEPVAGSFSHFAYKYWGDFP------GFLSGWNYWVLYVLVSMAELTAVGTYVHY 119
           GEM    P  GSF  +A + W D P      GFL+GW YW  +V+V   E  A  + V +
Sbjct: 69  GEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGASLVQF 128

Query: 120 WWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG 179
           W PGVP W  +LV    +   NL +VK++GE EFWFA IKV A++  +   G  ++    
Sbjct: 129 WLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAGLFVLGMWP 188

Query: 180 GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQ 239
           G  AS+++L  HGGF P+G   + T        + G E++ I AAE  EPQK++ +A + 
Sbjct: 189 GATASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETAEPQKAVARATSS 248

Query: 240 VIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVY 299
           VI R+L+FY+ S+ +++ L PWN  A   +P+V   + +     A ++N VVLTA LS  
Sbjct: 249 VITRVLVFYVGSVLLVVCLVPWNS-AGIATPYVSALNAMRIPAAAQIMNAVVLTAVLSAL 307

Query: 300 NSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALG 359
           NSG+YA+SRML+ L ++G+AP+AL ++ R GVP  AI  + L  +  V+++Y+ P +   
Sbjct: 308 NSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAVVMSYVSPDKVFA 367

Query: 360 LLMALVVAALVLNWALISLTHLKSR-RAMVAAGETLVFKSFWFPVSNWICLAFMALILVI 418
            L+       +  + LI+++ L+ R R    A   L  + + FP   W+ +A M  I+V 
Sbjct: 368 FLVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFPYLTWVAIAGMVGIVVA 427

Query: 419 LAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAARVVG 460
           +A  P     +LL    L ++   YA  R++   H AA  +G
Sbjct: 428 MAFIPDQRTPLLLGVASLGILVVAYAV-RQQLRKHAAAAPLG 468


Lambda     K      H
   0.327    0.140    0.440 

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: 502
Number of extensions: 27
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: 461
Length of database: 474
Length adjustment: 33
Effective length of query: 428
Effective length of database: 441
Effective search space:   188748
Effective search space used:   188748
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 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