GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Sphingopyxis indica DS15

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_089215766.1 CHB69_RS09450 FAD-binding protein

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_900188185.1:WP_089215766.1
          Length = 528

 Score =  472 bits (1215), Expect = e-137
 Identities = 254/523 (48%), Positives = 326/523 (62%), Gaps = 3/523 (0%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           +FD +++G GSAG   A RL+ D    VCL+EAG  +    + TP G    +P +  NW 
Sbjct: 3   QFDIIVIGGGSAGSAAAGRLAGDGRRRVCLVEAGGTNDIVRVKTP-GFMPFIP-KASNWQ 60

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           + T PQ GL GR+GYQPRG+ LGGSS+IN M+YIRG   D++ W  LG  GW + DVLP+
Sbjct: 61  YDTVPQRGLNGRIGYQPRGRGLGGSSAINAMVYIRGTAFDYDQWAELGATGWSYADVLPW 120

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAG 180
           F++SE +  G+ E+HG DG L V      +  S  FVESA         DFN  + EG G
Sbjct: 121 FKRSEGNERGADEWHGADGPLNVMDQRWPNVTSRRFVESAAALQLPRTADFNRPSNEGFG 180

Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240
            Y VT + G RWS A A+++P+R R+N  + T   VE I++   +A GV     G R  L
Sbjct: 181 LYQVTQKAGERWSAARAYVEPLRGRANFDIRTGALVEKILIEKGRAVGVAIRRGGRRETL 240

Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300
           RA   VILSAGAFGSP +LMLSG+G AA L   GI    +  GVG NLQDH D V  +++
Sbjct: 241 RAAGGVILSAGAFGSPQILMLSGVGPAAHLREHGIEVVRDRAGVGANLQDHIDYVSSWET 300

Query: 301 NDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIG 360
             T   G SL G  +M KA+F++  HR G + +  AEAG F K+ P L  PD+Q H V  
Sbjct: 301 RSTEPFGDSLGGTWRMVKAIFEHRLHRTGILTTCFAEAGGFWKSRPDLPAPDVQYHFVPA 360

Query: 361 TVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKG 420
            ++DH R    GHGFSCH CVLRP+S GSV LAS DP  AP IDP FL  D D+ATL  G
Sbjct: 361 MLEDHGRTRVKGHGFSCHACVLRPESRGSVTLASADPAAAPLIDPGFLTDDRDMATLRAG 420

Query: 421 YRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVV 480
            R+   I+A  P+A +G  D +   L +D  L  L+R R DT+YHP+G+C+MG D  AVV
Sbjct: 421 VRMMHRIVATPPLADYGGVDRHPVDLDDDAALDALIRDRADTVYHPVGSCRMGSDADAVV 480

Query: 481 DSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           D  L+++GIEGL V DASIMP LV GNTNA +IMI ERAA+++
Sbjct: 481 DPALKLNGIEGLWVADASIMPRLVSGNTNAPSIMIGERAADFV 523


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: 885
Number of extensions: 48
Number of successful extensions: 3
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: 528
Length adjustment: 35
Effective length of query: 491
Effective length of database: 493
Effective search space:   242063
Effective search space used:   242063
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