GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Neptunomonas antarctica S3-22

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_054342102.1 Nant_RS13025 alcohol dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_001305295.1:WP_054342102.1
          Length = 544

 Score =  420 bits (1079), Expect = e-122
 Identities = 235/535 (43%), Positives = 329/535 (61%), Gaps = 15/535 (2%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62
           +DY+IVGAGSAGCV+ANRLSADP+V+VCL+EAG   +SPL+  P G+  +   +  ++ F
Sbjct: 4   YDYIIVGAGSAGCVVANRLSADPAVSVCLIEAGGGGKSPLVSIPAGIFGLYGNKKYDYTF 63

Query: 63  KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122
           +  PQ  L  R     RGK LGGSS+IN M+YIRG+++D++ W  LG +GW + DVLP F
Sbjct: 64  EGVPQRHLNNRTMMVNRGKALGGSSAINSMVYIRGNKNDYDGWAKLGCQGWSYADVLPLF 123

Query: 123 RKSEMHHGG-SSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPDFNGATQEGAG 180
           ++ E +  G S++YHG +GEL V+ P + +   + FV++   AG   N DFN ATQ G G
Sbjct: 124 KQMEANQNGQSADYHGFNGELSVTKPQDPNPVDQVFVKAGKAAGLPENTDFNAATQFGLG 183

Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240
            YDV    G R S+ TAF+KPV  R NLT++T+T V S+ + G   TG++  + G+    
Sbjct: 184 IYDVKQHRGERVSSYTAFVKPVLSRPNLTLMTYTEVVSLQIQGDTVTGLEVEVNGNAQQW 243

Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300
           R  KEVIL AG   SP LL+ SGIG    L   GI  +  +PGVG+NLQDH D ++  +S
Sbjct: 244 RCNKEVILCAGTILSPRLLLASGIGDQTALSALGIECKQHVPGVGENLQDHVDSMVTVRS 303

Query: 301 NDTSLLGFSLSGGV-KMGKAMFDYARHRNGPVASNCAEAGAFLKT------DPGL--ERP 351
           + +  +G SL   +  +  A F Y   R G   +N  EAG F KT      +PG     P
Sbjct: 304 STSDSIGISLGTILPHIIPAPFKYWLARKGWWTTNYVEAGGFAKTKLAEAAEPGSADADP 363

Query: 352 DIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411
           D+Q H          +K   GHG+S   CVLRP+S G+V L++   R+   ID NF A +
Sbjct: 364 DVQFHLTPLYRSPRGKKFELGHGYSVFTCVLRPRSAGTVKLSNDGTRRNVLIDHNFFADE 423

Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH--NDEQLIELLRKRTDTIYHPIGT 469
            D   L++G +  R+I+A          +M + G H   DEQ+++ L   T T+YHP+GT
Sbjct: 424 RDQKVLIEGLKKAREILAAPEFDPLRGEEM-APGKHIQTDEQILDYLINTTTTVYHPVGT 482

Query: 470 CKMGQDEMAVVD-SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           CKMG DEMAVVD + L+V G++ LRV+DAS+MPTL+ GNT+A ++MIAE+ ++ I
Sbjct: 483 CKMGIDEMAVVDPATLKVKGMQNLRVMDASVMPTLISGNTSAPSMMIAEKGSQMI 537


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: 815
Number of extensions: 41
Number of successful extensions: 7
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: 544
Length adjustment: 35
Effective length of query: 491
Effective length of database: 509
Effective search space:   249919
Effective search space used:   249919
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