GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter permease (characterized, see rationale)
to candidate 8501893 DvMF_2608 inner-membrane translocator (RefSeq)

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Miya:8501893
          Length = 302

 Score =  269 bits (688), Expect = 5e-77
 Identities = 136/294 (46%), Positives = 201/294 (68%), Gaps = 11/294 (3%)

Query: 11  GLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGWVIL 70
           GL  GS+YALIALGYTMVYGII+LINFAHGEV M+GA T+    G +   + G P   IL
Sbjct: 13  GLTRGSIYALIALGYTMVYGIIELINFAHGEVYMMGAFTALIVAGAL--GIYGFPALAIL 70

Query: 71  LLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKPNYKPY 130
           ++A ++A +  A     +EK+AY+PLR +PRL+PLI+AIGMSI LQ   ++    ++ P+
Sbjct: 71  IIAAVVAVIYCAAYGLTLEKIAYKPLRDAPRLSPLISAIGMSIFLQNYVILAQTSDFMPF 130

Query: 131 PTMLPSSPF-EIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENPRVASL 189
           P ++P   F E     +  +++LI+  +A+++A+L   + +T +G+AMRATA+N ++A L
Sbjct: 131 PNLVPQPDFLEPIAHIMGASEVLIIVTSAISMAALTLFIKYTRMGKAMRATAQNRKMAML 190

Query: 190 MGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGIGNLAG 249
           +G+  D VIS TF+IG+ LAA+ G++ AS+ G     +GF+ G+KAFTAAV GGIG++ G
Sbjct: 191 LGIDADKVISLTFVIGSSLAAVGGVLIASHVGQVNFAIGFIAGIKAFTAAVLGGIGSIPG 250

Query: 250 AVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGE 303
           A++GG++LG  E+  +GYI         S Y D  AF +L++IL  RPSG+LG+
Sbjct: 251 AMLGGLVLGWCESFATGYI--------SSDYEDALAFALLVLILIFRPSGILGK 296


Lambda     K      H
   0.327    0.142    0.419 

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: 266
Number of extensions: 17
Number of successful extensions: 6
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: 309
Length of database: 302
Length adjustment: 27
Effective length of query: 282
Effective length of database: 275
Effective search space:    77550
Effective search space used:    77550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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