GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Ac3H11_909 Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25)

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_909
          Length = 374

 Score =  154 bits (388), Expect = 4e-42
 Identities = 83/236 (35%), Positives = 133/236 (56%), Gaps = 10/236 (4%)

Query: 38  VLAETGCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDIL 97
           V  + G    + D+SL I +GE+  ++G SG GK+TL+R    L     G I   GED  
Sbjct: 8   VSKQFGDFQALRDVSLDIQSGELIALLGPSGCGKTTLLRIIAGLETADVGTIHFSGEDTT 67

Query: 98  QLDMDALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCA----ERALHWI 153
            + +      R   +  VFQ + L  H +V +NVA+GL+V+  S++       ++ +  +
Sbjct: 68  DVHV------RERNVGFVFQHYALFRHMTVFENVAFGLRVKPRSERPSEAQIKKKVMDLL 121

Query: 154 NTVGLKGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLE 213
             V L     +YP QLSGG RQR+ LARALA +  ++L+DE F ALD  +R E++  L  
Sbjct: 122 KLVQLDWLAERYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLRR 181

Query: 214 LQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269
           L   LH T +F+THD +EA+ + +R+ ++  G++ Q G+P+++   PA  +V  F+
Sbjct: 182 LHDELHVTSIFVTHDQEEALEVADRVVVINQGRIEQSGSPQQVWDQPASPFVYGFL 237


Lambda     K      H
   0.321    0.138    0.387 

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: 243
Number of extensions: 17
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: 276
Length of database: 374
Length adjustment: 28
Effective length of query: 248
Effective length of database: 346
Effective search space:    85808
Effective search space used:    85808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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