GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Marinobacter adhaerens HP15

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF3112 HP15_3055 high-affinity leucine-specific leucine-specific-binding periplasmic protein of high-affinity branched-chain amino acid ABC transporter transport system periplasmic binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__Marino:GFF3112
          Length = 370

 Score =  172 bits (435), Expect = 2e-47
 Identities = 118/381 (30%), Positives = 193/381 (50%), Gaps = 24/381 (6%)

Query: 3   LKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62
           +K  +T V+   A  G   A  ++ +IG   P++G  A YG    +GARMAIE++NA G 
Sbjct: 5   VKKLVTAVSTSVALMGAGHAAAEI-QIGIAGPMTGPVAQYGDMQFSGARMAIEQINANGG 63

Query: 63  TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIP 122
            +G + +  E    DD  DPKQ    A  L +  V  V+GHL S +T PAS +Y D GI 
Sbjct: 64  VMGEELVAVEY---DDVCDPKQAVTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGIL 120

Query: 123 HVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVA 182
            VT A+T+P +T+ GY+  FR I  D+  G   A Y + +   + VAI+ D+  YG+G+A
Sbjct: 121 MVTPASTSPEITERGYELVFRTIGLDSMQGPVAARY-IASQNPERVAIVHDKQQYGEGIA 179

Query: 183 DVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQ 242
              + T    G+++   +  T    DF +++T +K  + D ++YGG  P+ G +LRQ   
Sbjct: 180 TAVRDTLKDAGVEIAMFEGITAGDKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQANS 239

Query: 243 LGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAK------- 295
             + + ++ G +G+   +I  +A  A        AEG   L  +P     KA+       
Sbjct: 240 ADL-DARFMGPEGVGNKDINTIAGEA--------AEG--LLVTLPPAFDQKAENQALVKA 288

Query: 296 YDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNG 355
           ++ K  +    +   +Y A  L+ + ++ A S DP      L + +F+    T+ ++  G
Sbjct: 289 FEDKGEDPSGPFVLTSYTAVQLVAEGIEAAGSTDPFDVAAALREGTFQTPIGTVEYDKAG 348

Query: 356 EMKNPAITLYV-YKDGKKTPL 375
           +MK+    +Y  + DG KTP+
Sbjct: 349 DMKSFEFVVYEWHSDGSKTPV 369


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: 379
Number of extensions: 17
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: 375
Length of database: 370
Length adjustment: 30
Effective length of query: 345
Effective length of database: 340
Effective search space:   117300
Effective search space used:   117300
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