GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Burkholderia phytofirmans PsJN

Align Amino acid:proton symporter (characterized, see rationale)
to candidate BPHYT_RS33330 BPHYT_RS33330 C4-dicarboxylate ABC transporter

Query= uniprot:A0A0N9WTL5
         (431 letters)



>FitnessBrowser__BFirm:BPHYT_RS33330
          Length = 435

 Score =  461 bits (1185), Expect = e-134
 Identities = 238/423 (56%), Positives = 301/423 (71%), Gaps = 2/423 (0%)

Query: 3   KNKLPRRIAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLVFA 62
           KN+L   I  G+ALGV+VG+ CH  A     AK IA YFS++TDIFLR++KMIIAPLVFA
Sbjct: 2   KNRLTFYIVAGMALGVIVGYVCHRSAAGAAEAKTIAGYFSIITDIFLRLVKMIIAPLVFA 61

Query: 63  TLVGGIASMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHATA 122
           TLV G+A M  +  V RIG R++ WFV AS+ SL +G+ L N  QPGAGL+M     +  
Sbjct: 62  TLVSGLAGMEGTSDVRRIGFRSVGWFVCASLFSLALGLALANALQPGAGLHMTQTS-SDV 120

Query: 123 AVPVNTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKR-AGYTRITD 181
           A  +NT   + K F+ H FP SI +AMA N+ILQI+VFS+ FG  L+ +K+    T +  
Sbjct: 121 ATGLNTAGLNFKDFVTHAFPSSIIDAMARNDILQILVFSVLFGVVLSAIKKDPRVTPLIA 180

Query: 182 SIEELAKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWAL 241
            I+ L   M K+TDYVM  APIGVF A+ASAIT  GL +L  YGKL+  FYLG++ LW +
Sbjct: 181 GIDALVPAMLKLTDYVMRLAPIGVFGALASAITVNGLDVLTTYGKLVGSFYLGLVTLWIV 240

Query: 242 LFGAGYLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLPL 301
           L   GY FLG+S++ L K +REP +LAFSTASSE+AYP+  E LE FG  K+V  F LPL
Sbjct: 241 LIFVGYAFLGKSIWRLLKAVREPAMLAFSTASSEAAYPRLTEKLEAFGIDKKVVGFTLPL 300

Query: 302 GYSFNLDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVAA 361
           GY+FNLDGSMMYQAFA +FIAQA+ ID+    Q+++LL LM++SKGMAGVAR SVVVVAA
Sbjct: 301 GYAFNLDGSMMYQAFAAIFIAQAFGIDMPLGAQIMMLLVLMLSSKGMAGVARGSVVVVAA 360

Query: 362 TLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSESHEEADEEEGEHAPA 421
             PMF+LP +G++LI+ IDQ LDM RTATNV+GNSIATAV+AK E+       +G  +PA
Sbjct: 361 IAPMFHLPPSGVVLILAIDQILDMGRTATNVIGNSIATAVIAKWEAKRAVKHIDGADSPA 420

Query: 422 RSR 424
             R
Sbjct: 421 LGR 423


Lambda     K      H
   0.325    0.138    0.392 

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: 491
Number of extensions: 13
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: 431
Length of database: 435
Length adjustment: 32
Effective length of query: 399
Effective length of database: 403
Effective search space:   160797
Effective search space used:   160797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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