GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Thiothrix lacustris DSM 21227

Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate WP_028487567.1 Q394_RS0100600 iron-containing alcohol dehydrogenase

Query= SwissProt::P0A9S1
         (382 letters)



>NCBI__GCF_000621325.1:WP_028487567.1
          Length = 403

 Score =  135 bits (340), Expect = 2e-36
 Identities = 117/386 (30%), Positives = 171/386 (44%), Gaps = 28/386 (7%)

Query: 13  FGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPT 72
           FG G +  L     + G +  +I    +         + + + AAG  W I   V   P+
Sbjct: 20  FGAGVLRKLPAIAAQYGKRLLIITGTSSFTASDAGKTLFNALQAAGFTWEIRR-VTHEPS 78

Query: 73  ITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAI-GIISNNPEFADVRSLEGLSPT---N 128
              V E +   Q    D +I IGGGSP D  KA+ G++       D   LEG+ P     
Sbjct: 79  PHWVDETVAGLQGDSFDAVIGIGGGSPLDAAKAVAGLLKPGNSVMD--HLEGVGPELPYQ 136

Query: 129 KPSVPILAIPTTAGTAAEVTINYV--ITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPP 186
             S P +A+PTTAGT +E T N V  ++ E   +K    D   + + A ID D++   PP
Sbjct: 137 GSSTPFIAVPTTAGTGSEATKNAVLSVSGEHGFKKSFRADKL-VAEYAIIDPDLLASCPP 195

Query: 187 ALKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKD--AGEEMAL 244
           A  AA G+DA T  +E Y++  +  LTDAL +  +E +  +L        D  A  +MA 
Sbjct: 196 AQIAANGMDAFTQLMEAYVSTRSNPLTDALALAGMEAVRDSLLAFYRDPADSVARGKMAY 255

Query: 245 GQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIAR 304
              ++G+  +  GLG VHG+  PLGAF+   HGV   +L+    R N D    +  D   
Sbjct: 256 ASLLSGICLAQTGLGSVHGVVAPLGAFHPIGHGVGCGMLVTEATRLNIDLLEARDADSPA 315

Query: 305 VMGVKVEGMSLEEARNA------------AVEAVFALNRDVGIPPHLRDVGVRKEDIPAL 352
           +    V G   EE   +             +  +    + + + P L D GV + DIP L
Sbjct: 316 LAKYVVIGKLFEETPPSLPLSGEEQEVAPLIHTLETWAKQLHL-PRLSDFGVTEADIPKL 374

Query: 353 -AQAALDDVCTGGNPREATLEDIVEL 377
            A +    + T  NP E T  DI  L
Sbjct: 375 VANSRGSSMKT--NPVELTDSDIANL 398


Lambda     K      H
   0.319    0.136    0.404 

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: 424
Number of extensions: 28
Number of successful extensions: 5
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: 382
Length of database: 403
Length adjustment: 31
Effective length of query: 351
Effective length of database: 372
Effective search space:   130572
Effective search space used:   130572
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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