GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Paraburkholderia bryophila 376MFSha3.1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_04063 H281DRAFT_04063 amino acid/amide ABC transporter substrate-binding protein, HAAT family

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Burk376:H281DRAFT_04063
          Length = 400

 Score =  374 bits (960), Expect = e-108
 Identities = 189/365 (51%), Positives = 253/365 (69%), Gaps = 4/365 (1%)

Query: 11  AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70
           AA+AA+A  AS +  VVKIGH AP++G  AH GKDNENGAR+A+EE+NAQG+TI G KI 
Sbjct: 35  AAVAASAAPAS-EAIVVKIGHAAPLTGGIAHLGKDNENGARLAVEEINAQGLTIDGHKID 93

Query: 71  FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130
            +L A+DDAADPK GTA AQKL D  V  VVGHLNSG +IPASK+Y+D  I  ++ ++TN
Sbjct: 94  LQLDAQDDAADPKAGTAVAQKLVDDHVVAVVGHLNSGVSIPASKIYSDASIVQISPSSTN 153

Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190
           P  T+ G+KTT+R++A D   G  LA YA   L  K +A++DD TAYG+G+AD F KT  
Sbjct: 154 PAYTQQGFKTTYRVVATDAQQGPALANYATKALGAKRIAVVDDATAYGKGLADEFAKTVE 213

Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250
           A G K+V  + T D+ATDF AILT IK+ +PDAI +GGMD  GGP  +Q   LG+   K 
Sbjct: 214 ASGAKIVAREATNDRATDFRAILTKIKSVHPDAIMFGGMDATGGPFAKQAAALGI-RAKI 272

Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310
            GGDG+CT ++ +LA  A  + N++C+E G +L+KM  G  ++ KY  ++    Q+Y+P+
Sbjct: 273 LGGDGVCTDKVGELAGTA--VQNLVCSEAGLALSKMDRGADFEKKYVDRFHTPVQIYAPF 330

Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370
           TYDA ++IVDAMKRANS++       +  + + GV   IAF+  G++K  AITLY +KDG
Sbjct: 331 TYDAVYVIVDAMKRANSIEAPKVLAAMPSTDYNGVIGRIAFDDKGDLKEGAITLYDFKDG 390

Query: 371 KKTPL 375
           KK  L
Sbjct: 391 KKAVL 395


Lambda     K      H
   0.315    0.131    0.375 

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: 445
Number of extensions: 14
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: 375
Length of database: 400
Length adjustment: 30
Effective length of query: 345
Effective length of database: 370
Effective search space:   127650
Effective search space used:   127650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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 (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