GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_2396 in Paraburkholderia bryophila 376MFSha3.1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_02161 H281DRAFT_02161 amino acid/amide ABC transporter substrate-binding protein, HAAT family

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02161 H281DRAFT_02161 amino
           acid/amide ABC transporter substrate-binding protein,
           HAAT family
          Length = 381

 Score =  394 bits (1011), Expect = e-114
 Identities = 195/375 (52%), Positives = 262/375 (69%), Gaps = 3/375 (0%)

Query: 1   MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60
           +Q  L ++  A + A    ++A + VVKIGHVAP++G  AH GKDNENGAR+A+EE+NA+
Sbjct: 5   IQKLLPISAAAMLFATLATSAAADTVVKIGHVAPLTGGIAHLGKDNENGARLAVEEINAK 64

Query: 61  GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120
           G+TIGG+KI  +L A+DDAADP+  T  AQKL D KV  VVGHLNSGT+IPASK+Y+D G
Sbjct: 65  GLTIGGQKITLQLDAQDDAADPRTATQVAQKLVDDKVVAVVGHLNSGTSIPASKIYSDAG 124

Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180
           I  ++ +ATNP  T+ G+KTT+R++A D   G  LA YA   LK+K+VAI+DD TAYGQG
Sbjct: 125 IVQISPSATNPAYTQQGFKTTYRVVATDAQQGPALANYAAKGLKVKSVAIVDDSTAYGQG 184

Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240
           +A+ F+KTA + G+ V+    T DKA DF AILT IK +NPDAI YGGMD  GGP  +Q 
Sbjct: 185 LANEFEKTAKSLGLNVMSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPFAKQA 244

Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY 300
           +QLG+   K   GDG+CT +++ LA  A    N++C+E G +L KM GG A++AKY  ++
Sbjct: 245 KQLGL-RAKVLAGDGVCTDKLSDLAGDA--TDNIVCSEAGMALEKMEGGPAFQAKYLKRF 301

Query: 301 PNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNP 360
               Q+Y+P+TYDA ++IVDAMKRA S DP      +  + +KGV     F+  G++K+ 
Sbjct: 302 GQPIQIYAPFTYDAVYIIVDAMKRAGSTDPAKILAAMPNTDYKGVIGQTTFDSKGDLKHG 361

Query: 361 AITLYVYKDGKKTPL 375
            I+LY YK GKKT L
Sbjct: 362 VISLYNYKSGKKTLL 376


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: 474
Number of extensions: 16
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: 381
Length adjustment: 30
Effective length of query: 345
Effective length of database: 351
Effective search space:   121095
Effective search space used:   121095
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 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