GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Skermanella stibiiresistens SB22

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_037461509.1 N825_RS34055 iron-containing alcohol dehydrogenase

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>NCBI__GCF_000576635.1:WP_037461509.1
          Length = 377

 Score =  194 bits (494), Expect = 3e-54
 Identities = 126/355 (35%), Positives = 187/355 (52%), Gaps = 17/355 (4%)

Query: 26  MADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLK 85
           +A+ G  + LI+ D  + K G+ G +  AL E +    ++  T  NPT E V   L + +
Sbjct: 24  LAELGIAKPLIIADEGVAKAGIVGQIT-ALLEGSASPPVFTRTPTNPTEEAVEDALAVYR 82

Query: 86  ENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYE----GVDRSAKPQLPMIAINTTAG 141
           E+ CD +I++GGGSP D AKG+AL+AA+ G +  Y     G+ R      P+IA+ TTAG
Sbjct: 83  EHGCDGLIAVGGGSPIDLAKGVALLAAHDGPLERYAAIRGGIPRITAAVAPVIAVPTTAG 142

Query: 142 TASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIE 201
           T SE+ R  +IT      K+  +  H+ P  +V D  L +G+P+ LTAATGMDA+TH +E
Sbjct: 143 TGSEVGRASLITLRDGR-KLGFISPHLIPKRAVCDPELTLGLPRWLTAATGMDAVTHCVE 201

Query: 202 AYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGY 261
            Y+S    P  +A AL  +    +N+  A  +GS+  AR  M  A    G+ F    LG 
Sbjct: 202 TYLSPRDNPPAEAIALDGLKRAVDNIEKAAANGSDRDARHQMMMAALEGGLTFQK-GLGA 260

Query: 262 VHAMAHQLGGF--YNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEG 319
           VHA++H LGG    +L HG  NAV+LP    FN   A A+     A +G+      DA+ 
Sbjct: 261 VHALSHPLGGLKDLSLHHGTLNAVILPVTLRFNQSHAEAKYAVIRATLGLAA----DADL 316

Query: 320 AEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNPIQATHEE 374
           A+        L+ ++ +P  L ++ V       +A  A++D    TN   AT E+
Sbjct: 317 AD----YFERLSGRLGLPKNLAEMGVTRAIVPAIARAAIEDHSHATNARPATVED 367


Lambda     K      H
   0.318    0.131    0.373 

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: 355
Number of extensions: 24
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 383
Length of database: 377
Length adjustment: 30
Effective length of query: 353
Effective length of database: 347
Effective search space:   122491
Effective search space used:   122491
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 (21.8 bits)
S2: 50 (23.9 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