GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Acidovorax sp. GW101-3H11

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate Ac3H11_2396 Extracellular ligand-binding receptor precursor

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2396
          Length = 375

 Score =  191 bits (486), Expect = 2e-53
 Identities = 119/369 (32%), Positives = 192/369 (52%), Gaps = 8/369 (2%)

Query: 1   MNYKLSLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGG 60
           +  KL+++ A+AA A  AS  +  + +    P++G  A +G+  + G   A+ ++NA G 
Sbjct: 3   LKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62

Query: 61  VLG-QKLKLEV--GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVL 117
            +G +K+K E+   DDA DPKQ  A A +L  A V  V GH  SG++IPAS+VY + G+ 
Sbjct: 63  TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIP 122

Query: 118 QISPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLA 177
            ++ A+TNP LT+   K  FR+   D+  G     Y ++  K K VAI+ D++AYG+G+A
Sbjct: 123 HVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVA 182

Query: 178 DETQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKD 237
           D  +K   A G K    +  T    D+ A+++ +K +  D ++ GG   + G + RQM+ 
Sbjct: 183 DVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQ 242

Query: 238 QGL-NAPIVSGDALVTNEYWAITGPA---GENTMMTFGPDPREMPEAKEAVEKF-RKAGY 292
            G+ N     GD + T+E   +   A   G       G    +MP       K+  K   
Sbjct: 243 LGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPN 302

Query: 293 EPEGYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAY 352
           + + Y+ YTY A  +  +A K+ANS D       L K+S+  V   I F+  G++ +PA 
Sbjct: 303 QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAI 362

Query: 353 VWYRWNNGQ 361
             Y + +G+
Sbjct: 363 TLYVYKDGK 371


Lambda     K      H
   0.312    0.129    0.366 

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: 356
Number of extensions: 19
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: 366
Length of database: 375
Length adjustment: 30
Effective length of query: 336
Effective length of database: 345
Effective search space:   115920
Effective search space used:   115920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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