GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natD in Burkholderia phytofirmans PsJN

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate BPHYT_RS15605 BPHYT_RS15605 ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15605 BPHYT_RS15605 ABC
           transporter permease
          Length = 316

 Score =  134 bits (338), Expect = 2e-36
 Identities = 93/315 (29%), Positives = 167/315 (53%), Gaps = 40/315 (12%)

Query: 1   MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGV- 59
           MDI  IQ ++NG+ +GS+ A+ A+G T+ YGIL + NFAHGD L +GA +   ++  GV 
Sbjct: 1   MDI-FIQQVLNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVA--LSAIGVL 57

Query: 60  -----------NIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFL 108
                       + +++I+A +    V    E++ +  +R  +A     +I +IG+++ L
Sbjct: 58  QNHFPGLGNVPTLIIALIIAAIVCAAVGYTIERVAYRPLR--KAPRLAPLITAIGVSILL 115

Query: 109 RNGIILIWGGRNQNY-NLPITPALDIF-------GVKVPQNQLLVLALAVLSIGALHYLL 160
           +   ++IW      +  L  T  L++        G  +   +++++ +A L +G L  L+
Sbjct: 116 QTLAMMIWSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMGGLLLLV 175

Query: 161 QNTKIGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSM----YGLITAVRP 216
             TK+G+AMRA+A++   A + G++   VI  T++I   + +L G M    YG       
Sbjct: 176 HKTKLGRAMRAIAENPGNASLMGVNPNFVISATFMIGSALAALAGVMIASEYG---NAHF 232

Query: 217 NMGWFLILPLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPFL--------GSQYKQGVA 268
            MG+   L  F + +LGGIGN  GA+    I+G+++++   ++        GS Y+   A
Sbjct: 233 YMGFIPGLKAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFA 292

Query: 269 LLIMILVLLIRPKGL 283
            +++I+VL+ RP GL
Sbjct: 293 FIVLIIVLVFRPSGL 307


Lambda     K      H
   0.328    0.144    0.426 

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: 273
Number of extensions: 19
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: 288
Length of database: 316
Length adjustment: 27
Effective length of query: 261
Effective length of database: 289
Effective search space:    75429
Effective search space used:    75429
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: 48 (23.1 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