GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00890 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_2924 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2924 Branched-chain amino
           acid transport system permease protein LivM (TC
           3.A.1.4.1)
          Length = 418

 Score =  269 bits (687), Expect = 1e-76
 Identities = 158/355 (44%), Positives = 219/355 (61%), Gaps = 47/355 (13%)

Query: 4   TKTNWIIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVA 62
           T   WI+  +AL+V  L+   FG+   V IA L L+YV+L LGLNIVVG AGLLDLGYV 
Sbjct: 89  TTQRWIV--LALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVG 146

Query: 63  FYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLK 122
           FYAVGAY +AL++                +    S WI +P+A ++AA FG +LG P L+
Sbjct: 147 FYAVGAYSYALLS----------------HYFGLSFWICLPIAGMMAATFGFLLGFPVLR 190

Query: 123 LRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL------ 176
           LRGDYLAIVTLGFGEIIR+FL NL    ++T GP G+  I+    FGL   ++       
Sbjct: 191 LRGDYLAIVTLGFGEIIRLFLRNL---TDITGGPNGISNIEKPTFFGLTFERKAAEGLQT 247

Query: 177 --EVFGFDINSVTLYYYLFLV---LVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGI 231
             E FG + NS+    +L+LV   L + ++ +  RL    IGRAW A+REDEIA +A+G+
Sbjct: 248 FHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGL 307

Query: 232 NTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVI 291
           N   +KL AF +GA+F G +G+ F A QG V+PESF+ +ES +I+A+VVLGG+G   GVI
Sbjct: 308 NPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVI 367

Query: 292 LGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
           L A+++  LPE++R              + +  R L+    M+++M+ RP+GL P
Sbjct: 368 LAAIVMILLPEMMR--------------EFSEYRMLMFGALMVLMMIWRPQGLLP 408


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: 416
Number of extensions: 20
Number of successful extensions: 4
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: 418
Length adjustment: 30
Effective length of query: 328
Effective length of database: 388
Effective search space:   127264
Effective search space used:   127264
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: 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, 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