GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Mariniradius saccharolyticus AK6

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_008630494.1 C943_RS17395 hypothetical protein

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000330725.2:WP_008630494.1
          Length = 532

 Score =  435 bits (1119), Expect = e-126
 Identities = 243/532 (45%), Positives = 332/532 (62%), Gaps = 12/532 (2%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60
           M FDY+I+GAGSAGCVLANRLS +   +V LLEAG  D    IH P G    L     +W
Sbjct: 1   MTFDYIIIGAGSAGCVLANRLSENSKNSVLLLEAGNPDTKKDIHIP-GAYTNLHRSDTDW 59

Query: 61  AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120
           AF T PQ  + GR  + PRGK LGGSSS N M Y+RG+  DF++W+ALGN+GW + DVLP
Sbjct: 60  AFWTEPQEHVDGRRIFIPRGKTLGGSSSTNAMAYVRGNPADFDEWEALGNKGWSYKDVLP 119

Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGA 179
           +F+KSE +    ++Y G +G L+V  + + H   + F+++   +G   NPD+NG  Q GA
Sbjct: 120 FFQKSEHNENLDAKYCGKNGPLHVGYSKQPHFLGQKFLDACSASGIPQNPDYNGPDQIGA 179

Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIK-GSRV 238
                TI++  R STATAFLKP+ +R NLTV T + V  IVL G +A  V+ L K G +V
Sbjct: 180 AMLQFTIKNNVRQSTATAFLKPILNRPNLTVKTGSRVSRIVLEGNKAVAVEVLTKDGKKV 239

Query: 239 HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298
                KE+ILSAGA  SP +L+LSGIG    L   GI P++ LPGVGQNLQDH    +  
Sbjct: 240 TYTCEKEIILSAGAIQSPQILLLSGIGDRDYLGHFGIEPKNHLPGVGQNLQDHIWSGVIA 299

Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLH-S 357
           +SN  +         ++MGKA+F Y   + GP+  +   A AFL +D    R DIQ H +
Sbjct: 300 RSNVPT--NNHTLKPLEMGKALFRYLLFKKGPLGESPLTANAFLSSDGRSSRQDIQFHFA 357

Query: 358 VIGTVDDHNRKLH------WGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411
           V G  +D++  ++         GFS  V +LRP+S G +GL S DP   P I PN L+ +
Sbjct: 358 VTGIAEDYSTDIYDLSTFPKESGFSIMVILLRPESRGFIGLKSADPLAEPIIQPNLLSQE 417

Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCK 471
           +D+  LL G +  ++++ Q+P+  +   ++Y       + L   LRK  +T+YHP+GTCK
Sbjct: 418 EDIKKLLWGLKKAKEVMDQSPLKQYHQGNVYLPWDFRKDALEWHLRKSLETLYHPVGTCK 477

Query: 472 MGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           MGQD+ +VVD +LRVHGI+GLR+ DASIMPT++ GNTNAA IMI E+AA+ +
Sbjct: 478 MGQDDASVVDEKLRVHGIKGLRIADASIMPTIISGNTNAACIMIGEKAADMV 529


Lambda     K      H
   0.319    0.137    0.419 

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: 731
Number of extensions: 37
Number of successful extensions: 6
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: 526
Length of database: 532
Length adjustment: 35
Effective length of query: 491
Effective length of database: 497
Effective search space:   244027
Effective search space used:   244027
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: 52 (24.6 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