GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-c in Halomonas xinjiangensis TRM 0175

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate WP_043530172.1 JH15_RS11025 cytochrome c

Query= BRENDA::D2SZY5
         (472 letters)



>NCBI__GCF_000759345.1:WP_043530172.1
          Length = 435

 Score =  348 bits (894), Expect = e-100
 Identities = 190/438 (43%), Positives = 263/438 (60%), Gaps = 15/438 (3%)

Query: 1   MMINRLKAALGAVAVGLLAGTSLAHAQNAD---EDLIKKGEYVARLGDCVACHTSLNGQK 57
           ++I  L  AL ++ +G  A  + A AQ+ D   + LI+KGEY+AR GDCVACHT+   + 
Sbjct: 3   IVIRLLSIALLSLFLGSQATHAQAPAQDRDPSRDALIEKGEYLARAGDCVACHTADENKM 62

Query: 58  YAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFA 117
           +AGGL+++TPIGTIYSTNITPDP  GIG YT ++F  A+R GV   G  LYPAMPYPS+A
Sbjct: 63  FAGGLAMQTPIGTIYSTNITPDPETGIGRYTLEDFTRAMREGVTPAGHALYPAMPYPSYA 122

Query: 118 RMTQDDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGT 177
           R+T +DM+ALY YF+HGV+PI Q+N  + I WP+SMRWPL IW  +F P    F P P  
Sbjct: 123 RITDEDMQALYVYFLHGVEPIQQQNRDSVIPWPLSMRWPLRIWSWMFTPDETGFDPDPER 182

Query: 178 DAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDP 237
             E  RG YLV G GHCGACHTPRG   QE+   A G   FL GG +++ W + ++ +D 
Sbjct: 183 SDEWNRGAYLVEGLGHCGACHTPRGLAYQEQGFKA-GDNGFL-GGEMVEGWYSFNITSDS 240

Query: 238 VLGLGRWSDEDLFLFLKSGRTDHSA-AFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPV 296
             G+G W D+++  +L+ G     A A G M +V+G S +Y  DADL+A+  Y+KS+PP+
Sbjct: 241 EHGIGGWRDDEIVAYLRDGAVPGKAHAAGPMGEVIGHSLRYLDDADLYAIATYLKSVPPI 300

Query: 297 ---PPARGDYSYDASTAQMLDSNNFSGN---AGAKTYVEQCAICHRNDGGGVARMFPPLA 350
               P+R      A   + +D   F  +     AK Y+  CA CH + G G  R  P L 
Sbjct: 301 SDPEPSRFGQGEPADDVERMDDPGFVASPQGQAAKRYLTTCAYCHGDRGEGSRRGDPSLF 360

Query: 351 GNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGN 410
            + VV S +  ++  ++++ GV   TN     V MP Y + L D+Q+A +VN++   +GN
Sbjct: 361 NSSVVGSTHLNNLVRVILE-GVARETN--QGQVTMPGYADELDDEQMAQLVNYLVDRFGN 417

Query: 411 RAPANTTAADIQKLRLDH 428
                    DI  +R  H
Sbjct: 418 PEAETLAPEDIAAMRSTH 435


Lambda     K      H
   0.318    0.135    0.430 

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: 701
Number of extensions: 46
Number of successful extensions: 8
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: 472
Length of database: 435
Length adjustment: 33
Effective length of query: 439
Effective length of database: 402
Effective search space:   176478
Effective search space used:   176478
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: 51 (24.3 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