GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Pseudomonas fluorescens FW300-N2E3

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate AO353_13535 AO353_13535 urea ABC transporter permease subunit UrtC

Query= uniprot:A0A159ZYE0
         (418 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_13535 AO353_13535 urea ABC
           transporter permease subunit UrtC
          Length = 359

 Score =  105 bits (261), Expect = 3e-27
 Identities = 94/332 (28%), Positives = 149/332 (44%), Gaps = 56/332 (16%)

Query: 107 FFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLS------- 159
           F  S   + +A  IL Y ++ L L++V G AGLL LG+  F+A+G Y+  +         
Sbjct: 44  FHVSAYTLTLAGKILCYAIVALALDLVWGYAGLLSLGHGLFFALGGYAMGMYLMRQASGD 103

Query: 160 ----------------HYFGLSFWI---CLPIA--GMMAATFGFLLGFPVLRLRGDYLAI 198
                           ++ G S +I   CL +   G++A  FGF       R++G Y +I
Sbjct: 104 GLPAFMTFLSWTELPWYWTGTSSFIWAMCLVVLAPGLLALVFGFFAFRS--RIKGVYFSI 161

Query: 199 VT--LGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEY 256
           +T  L F  ++ LF RN T   GG NG +N      FG+T     A              
Sbjct: 162 MTQALTFAGML-LFFRNETGF-GGNNGFTNFCTILGFGITEPGTRA-------------- 205

Query: 257 NSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSA 316
                   L++  +LL +A+LF+  RL +   GR   ALR+ E      G +P   KL  
Sbjct: 206 -------VLFVATVLLLVASLFIGWRLAQSKFGRVLTALRDAENRLMFCGYDPRGFKLFV 258

Query: 317 FTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVIL-AAIVMIL 375
           + L A   G AG+ +  + G++ P   +   S      V LGG G+ +G +L A +V  +
Sbjct: 259 WVLSAVLCGLAGALYVPQVGIINPSEMSPTNSIEAAVWVALGGRGTLIGPLLGAGVVNGM 318

Query: 376 LPEMMREFSEYRMLMFGALMVLMMIWRPQGLL 407
                  F EY +   GAL +++ ++ P+G++
Sbjct: 319 KSWFTVAFPEYWLFFLGALFIVVTLYLPKGVI 350


Lambda     K      H
   0.331    0.145    0.439 

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: 453
Number of extensions: 23
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: 418
Length of database: 359
Length adjustment: 30
Effective length of query: 388
Effective length of database: 329
Effective search space:   127652
Effective search space used:   127652
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 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, 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