GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Shewanella halifaxensis HAW-EB4

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012275184.1 SHAL_RS00270 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000019185.1:WP_012275184.1
          Length = 307

 Score = 96.7 bits (239), Expect = 6e-25
 Identities = 84/268 (31%), Positives = 120/268 (44%), Gaps = 37/268 (13%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           +T++K   L   FG L AI +  FE ++G I   +GPNG GKTT    +TG   PT G I
Sbjct: 3   ETVIKTTQLCRDFGSLKAIQNLDFEVEKGQIYGFLGPNGCGKTTAIRMLTGLLLPTAGDI 62

Query: 72  TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENL-LVAQHNKLMKASGY 130
                   + L  +LP        ++    Q   L+  LTV ENL  +A+          
Sbjct: 63  --------EILGLQLPRDAEKLRLKIGYMTQKFSLYDDLTVKENLKFIAK---------- 104

Query: 131 TILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190
            I GL      + + A   EL    L    L  +AD  AG +  G ++RL +A A    P
Sbjct: 105 -IYGL----SRREQTARIQEL----LNTYGLEQKADQLAGSMSGGQKQRLGLAAATMHKP 155

Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250
           ELL LDEP + ++P         L  +  E GT+IL+  H M    E    + +LE G K
Sbjct: 156 ELLFLDEPTSAVDPENRRDFWEKLFDL-CEQGTTILVSTHYMDEA-ERCHKLAILEAGVK 213

Query: 251 ISDGTPDHVKNDPRVIAAYLGVEDEEVE 278
             DG+P+ +  +       +G +  EVE
Sbjct: 214 RVDGSPEQLMQN-------MGAQVVEVE 234


Lambda     K      H
   0.318    0.136    0.386 

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: 165
Number of extensions: 11
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: 292
Length of database: 307
Length adjustment: 27
Effective length of query: 265
Effective length of database: 280
Effective search space:    74200
Effective search space used:    74200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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