GapMind for catabolism of small carbon sources

 

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

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043531345.1 JH15_RS13880 FAD-binding protein

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000759345.1:WP_043531345.1
          Length = 554

 Score =  382 bits (981), Expect = e-110
 Identities = 225/543 (41%), Positives = 311/543 (57%), Gaps = 20/543 (3%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           EFDY++VGAG+AGC+LANRLSADP+  V L+EAG  D    IH P+G    +     +W 
Sbjct: 8   EFDYIVVGAGTAGCLLANRLSADPNNRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWL 67

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDDVLP 120
           F+T P  GL GR    PRGK LGG SSINGMIY+RG   D++ W +  G++ W +++ L 
Sbjct: 68  FRTEPDAGLNGRSLLYPRGKTLGGCSSINGMIYMRGQARDYDHWAEVTGDDAWRWENCLA 127

Query: 121 YFRKSEMHH----GGSSE-----YHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNPD 170
            F + E H+    GG+++     +HG  GE  V    +R    + F ++A +AG     D
Sbjct: 128 DFTRHEDHYRLDAGGNADAQHRDFHGHGGEWRVEKQRHRWQILDDFADAAEQAGIPKTDD 187

Query: 171 FNGATQEGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHV------ESIVLLGK 224
           FN    EG GY++V  R G RW+TA AFL+P   R +   L H+ +      E+      
Sbjct: 188 FNRGNNEGVGYFEVNQRAGWRWNTAKAFLRPACERRDNFTLWHSTLAHKLEFETGAHGTP 247

Query: 225 QATGVQALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGV 284
           + TGVQ   +G+   +RAR+EVIL +GA GSP LL LSGIG AA L   GI   H+LPGV
Sbjct: 248 RCTGVQVERQGTVSRVRARREVILCSGAIGSPQLLQLSGIGPAALLHKHGIPVVHDLPGV 307

Query: 285 GQNLQDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKT 344
           G+NLQDH  +   Y+      L    S     G    +Y   R+GP++   ++ GAF ++
Sbjct: 308 GENLQDHLQIRSVYRVTGGKTLNTLASTLWGKGLIGLEYLLTRSGPMSMAPSQLGAFTRS 367

Query: 345 DPGLERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRID 404
            P    P+IQ H    +++   + LH     +  VC L P S G V + S DPR+AP I 
Sbjct: 368 SPEHAEPNIQYHVQPLSLEAFGQPLHDYPAITASVCNLSPTSRGHVRIKSRDPREAPCIS 427

Query: 405 PNFLAHDDDVATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTI 463
           PN+L+ ++D        R+TR I+AQ   A +   ++       +DE+L  L      TI
Sbjct: 428 PNYLSTEEDRKVAADSLRVTRRIVAQPAFARYRPEEVKPGMQYQSDEELTRLAGDIATTI 487

Query: 464 YHPIGTCKMGQ--DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521
           +HP GT +MG+  D +AVVDS LRV G++GLRVVDA +MPT+  GNTN+  +MIAE+AA 
Sbjct: 488 FHPAGTTRMGRADDPLAVVDSHLRVRGVDGLRVVDAGVMPTITRGNTNSPTLMIAEKAAG 547

Query: 522 WIA 524
           WIA
Sbjct: 548 WIA 550


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: 857
Number of extensions: 40
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: 526
Length of database: 554
Length adjustment: 35
Effective length of query: 491
Effective length of database: 519
Effective search space:   254829
Effective search space used:   254829
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