GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Lutibaculum baratangense AMV1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_023430731.1 N177_RS02905 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>NCBI__GCF_000496075.1:WP_023430731.1
          Length = 375

 Score =  150 bits (378), Expect = 7e-41
 Identities = 115/370 (31%), Positives = 180/370 (48%), Gaps = 21/370 (5%)

Query: 10  VAAIAAAA----GVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIG 65
           VAAIA AA    G A AQE  VKIG + P+SG  +  G    NG ++AI++ NA+   +G
Sbjct: 13  VAAIALAAVVATGAADAQE-TVKIGFIGPLSGGNSQQGLTARNGFQLAIDQANARE-DLG 70

Query: 66  GKKIKFELVAEDDAADPKQGTAAAQKLC-DAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124
               K E V +DDA++P+ G +AA KL  D  V  V GH NS   +  + V    GIP V
Sbjct: 71  ---FKIEGVIQDDASNPQTGVSAALKLTNDPAVIAVTGHWNSPVALATAPVITRAGIPFV 127

Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184
              A +P +T+       R++         LA +A + +  + +AI+ D + YG      
Sbjct: 128 IWGAISPKITETNNPLLARVVPTLVNTNEPLAAWAAEEIG-QNIAIVSDTSDYGMANVAA 186

Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244
           F+K     G  +   +      TDF A LT IK+ NPDAI++GG+  + G + +QM+++G
Sbjct: 187 FRKPFEEAGGTITSVETAPVGTTDFRATLTKIKSDNPDAIYFGGVVTEAGLVRQQMKEVG 246

Query: 245 MGNVKYFGGDGICTSEIAKLAAGAK--TLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPN 302
           + +V   G DG    E  K+A  A   T+  ++       L +M      +A   A +  
Sbjct: 247 L-DVPMIGVDGFHDPEFIKIAGDAAEGTISGIMKETENEKLVEMN-----EAYAAAGFAE 300

Query: 303 QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPA- 361
               Y+   YDA  +I+ A++ A + D       +    + G     +F+ NG+ K P  
Sbjct: 301 PVGTYTKNAYDAANIIIAAIEEAGT-DRAAVGEAIRAMEYDGAMGHTSFDENGQTKLPVD 359

Query: 362 ITLYVYKDGK 371
           + L V ++G+
Sbjct: 360 LELRVVRNGQ 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: 326
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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 24 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