GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Desulfovibrio vulgaris Hildenborough

Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein

Query= uniprot:Q1MDE9
         (367 letters)



>MicrobesOnline__882:206137
          Length = 376

 Score =  209 bits (533), Expect = 7e-59
 Identities = 126/357 (35%), Positives = 197/357 (55%), Gaps = 11/357 (3%)

Query: 6   LTATLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKV 65
           +T+ L+A+ AFA      + +GL+ PLTG  A+ G  ++N  +   +E+NK GGI G KV
Sbjct: 13  VTSLLMAATAFAA---GPVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNKAGGINGNKV 69

Query: 66  VLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAP 125
            L + DD G+P+    AA K+   G+  V+G   S V     ++  E G+  +   +T  
Sbjct: 70  ELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIAQIATGSTNV 129

Query: 126 DLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNA 185
            LT++GL   LRTC RDD+Q  VAAK V+KN   K VA+++D  +Y KGLAD  KA L+ 
Sbjct: 130 RLTEKGLKLFLRTCPRDDEQGRVAAK-VIKNKGYKAVALLHDNSSYAKGLADETKALLDK 188

Query: 186 GGITEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIG 245
            G   V  DA+TPG++D++A+ T++K+   D+++F GY+PE G+L RQ  ++  N  ++G
Sbjct: 189 DGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKMEMKWNVPMMG 248

Query: 246 GDGLSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAA-----KNIPAEAFTLNA 300
           GD  +N +   I   AA    F  +    +  D+  A   LAA       +P   +++ A
Sbjct: 249 GDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNALPNSVWSVLA 308

Query: 301 YAAVEVLKAGIEKAGSAEDAEAVATALKDG-KEIPTAIGKVTYGETGDLTSQSFSLY 356
             A +V+   ++K G A D   +AT LK   K  P   G++++ E GD     + +Y
Sbjct: 309 GDAFKVIVEAVQKGGKA-DGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGDLYRVY 364


Lambda     K      H
   0.312    0.131    0.362 

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: 364
Number of extensions: 21
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: 367
Length of database: 376
Length adjustment: 30
Effective length of query: 337
Effective length of database: 346
Effective search space:   116602
Effective search space used:   116602
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