GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1694 in Shewanella loihica PV-4

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 5210164 Shew_2608 inner-membrane translocator (RefSeq)

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__PV4:5210164 Shew_2608 inner-membrane
           translocator (RefSeq)
          Length = 357

 Score =  159 bits (401), Expect = 1e-43
 Identities = 102/332 (30%), Positives = 173/332 (52%), Gaps = 41/332 (12%)

Query: 19  PLILQS-FGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASP 77
           PL+L   F   +++I+ L +     ALGLNI+VG+ G + LG+ AF+  GA+     AS 
Sbjct: 43  PLVLDGYFLTLFIQISYLGIA----ALGLNILVGFTGQISLGHGAFFGFGAF-----ASA 93

Query: 78  HLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGE 137
            L  +F           +  +   IP+A  L    G M G P  +++G YLAI TL    
Sbjct: 94  WLNTSF-----------NIPVVFCIPLAGFLTMGVGMMFGMPAARIKGLYLAIATLAAQF 142

Query: 138 IIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLV 197
           II+ F    +     + G  G             +   + +FGFD ++   +Y++ L  +
Sbjct: 143 IIQDFFGRAEW---FSGGSSGA------------MAAPVSLFGFDFDTDMSFYFIALFAL 187

Query: 198 VVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGA 257
           V   I    L  SR GRA++A+R+  ++A+ MG+     +LL+FG+ + + G+ GA++  
Sbjct: 188 VFMYIWGCNLMRSRDGRAFVAVRDHYLSAEIMGVKLNKYRLLSFGISSFYAGIGGALYAH 247

Query: 258 FQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDG 317
           + G+VS E F+++ S+  +AMV++GG+G I G ++G V +  LPEVL  + G ++    G
Sbjct: 248 YLGYVSSEGFTILMSIQFLAMVIIGGLGSIKGTLMGVVFMVLLPEVLEGMVGLMKYTDYG 307

Query: 318 RLDS-----AILRQLLIALAMIIIMLLRPRGL 344
            L       A ++++ I L +I+ ++  P GL
Sbjct: 308 NLPMVTDGLAYIKEMAIGLVIILFLIFEPEGL 339


Lambda     K      H
   0.328    0.144    0.430 

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: 311
Number of extensions: 19
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: 358
Length of database: 357
Length adjustment: 29
Effective length of query: 329
Effective length of database: 328
Effective search space:   107912
Effective search space used:   107912
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: 49 (23.5 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