GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Corynebacterium deserti GIMN1.010

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_053544074.1 CDES_RS02230 ABC transporter ATP-binding protein

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



>NCBI__GCF_001277995.1:WP_053544074.1
          Length = 350

 Score =  156 bits (394), Expect = 7e-43
 Identities = 88/223 (39%), Positives = 131/223 (58%), Gaps = 6/223 (2%)

Query: 47  GVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALRE 106
           G+  + + +   E   ++G SGSGK+T++R     + PTSG++ + G D+  +    L E
Sbjct: 19  GLESIDIDVNPEEFVALIGPSGSGKTTMLRTIAGFVQPTSGSVHIGGNDMTHV----LPE 74

Query: 107 FRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYP 166
            RR  + MVFQ   + PH +V  NV Y L  RGE K   + R    +  VGL G+ ++ P
Sbjct: 75  NRR--MGMVFQQHAVWPHMTVAKNVGYPLARRGEKKASISSRVDRVLALVGLDGFGSRKP 132

Query: 167 HQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFIT 226
             LSGG RQRV LARA+ AD  ++L+DEA SALD  +R  ++ +L+ L +    T V +T
Sbjct: 133 ASLSGGQRQRVALARAIVADPAVLLLDEALSALDEPLRDALRRELVALTRREGLTTVHVT 192

Query: 227 HDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269
           HD  EA+ I +RI +L +G++ QV  P E+L +PA   V RF+
Sbjct: 193 HDRAEAMSIADRIVVLDNGQIQQVAPPAELLKTPATADVARFI 235


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: 192
Number of extensions: 6
Number of successful extensions: 2
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: 350
Length adjustment: 27
Effective length of query: 249
Effective length of database: 323
Effective search space:    80427
Effective search space used:    80427
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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