GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natD in Burkholderia phytofirmans PsJN

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS31740 BPHYT_RS31740 ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS31740 BPHYT_RS31740 ABC
           transporter permease
          Length = 316

 Score =  141 bits (355), Expect = 2e-38
 Identities = 97/307 (31%), Positives = 165/307 (53%), Gaps = 35/307 (11%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS--------G 56
           Q I NG+ +GS+ A+ A+G T+ YGIL + NFAHGD + + A +   A T         G
Sbjct: 6   QQIINGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAITVLQDHFPELG 65

Query: 57  INLWLSMALGCVGTIIAM--FIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIW 114
               L +AL     + AM  +  E + ++P+R  RA     +I +IG+++ L+   ++IW
Sbjct: 66  HVPTLLIALILAAAVCAMVGYTIEKVAYRPLR--RAPRLAPLITAIGVSILLQTAAMIIW 123

Query: 115 GGNNQNYR--VPIVP------AQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKA 166
           G N   +   +P  P      +++  G       + ++ +A   M  L L++ RTK+G+A
Sbjct: 124 GRNPLAFPQLLPTAPLNLIQASENHPGAVISLTEIAIVVVAFFVMAGLLLLVHRTKLGRA 183

Query: 167 MRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSM----YGLMTTLKPNMGWFLIL 222
           MRA+A+N ++A + G+N  +V+  T+++ + L AL G M    YG        MG+   L
Sbjct: 184 MRAIAENPNVASLMGVNPGFVISATFMIGSALAALAGVMIASEYG---NAHFYMGFIPGL 240

Query: 223 PMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW--------FGTSYKMGVALLLMIIIL 274
             F + +LGGIGN  GA+ GG+I+G+ +++   +        FG++Y+   A +++I +L
Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLVEQLGAGYIGTLTGGVFGSNYQDVFAFVVLIAVL 300

Query: 275 FIRPQGL 281
             RP GL
Sbjct: 301 VFRPSGL 307


Lambda     K      H
   0.329    0.143    0.450 

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: 188
Number of extensions: 10
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: 286
Length of database: 316
Length adjustment: 27
Effective length of query: 259
Effective length of database: 289
Effective search space:    74851
Effective search space used:    74851
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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