GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Pedobacter sp. GW460-11-11-14-LB5

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

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



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  127 bits (318), Expect = 3e-34
 Identities = 81/198 (40%), Positives = 111/198 (56%), Gaps = 2/198 (1%)

Query: 48  VNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREF 107
           +  +SL I  GE   +MG SGSGKSTL+     L  P+SG  +++G ++  +  DAL E 
Sbjct: 25  LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEV 84

Query: 108 RRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPH 167
           R  +I  VFQ+F LLP  + LDNVA  L   G SK+    RA   +  VGL    +  P+
Sbjct: 85  RNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPN 144

Query: 168 QLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITH 227
           +LSGG RQRV +ARAL  +  IIL DE    LD     E+   LLE   +   TI+ +TH
Sbjct: 145 ELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMG-LLEEIHSKGNTIILVTH 203

Query: 228 DLDEAVRIGNRIAILKDG 245
           + D A +  +RI  ++DG
Sbjct: 204 EEDIA-QHAHRIVRMRDG 220


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: 166
Number of extensions: 8
Number of successful extensions: 1
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: 252
Length adjustment: 25
Effective length of query: 251
Effective length of database: 227
Effective search space:    56977
Effective search space used:    56977
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: 47 (22.7 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