GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Jannaschia aquimarina GSW-M26

Align furfuryl alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043917880.1 jaqu_RS05220 alcohol dehydrogenase AdhP

Query= metacyc::MONOMER-17184
         (342 letters)



>NCBI__GCF_000877395.1:WP_043917880.1
          Length = 340

 Score =  434 bits (1116), Expect = e-126
 Identities = 221/340 (65%), Positives = 258/340 (75%), Gaps = 2/340 (0%)

Query: 1   MPAMMKAAVVRAFGAPLTIDEVPVPQPGPGQVQVKIEASGVCHTDLHAADGDWPVKPTLP 60
           MP+ MKAAVV  F  PL I EV  P    G++ VKIEA GVCHTDLHAA GDWPVKP  P
Sbjct: 1   MPSTMKAAVVTDFSKPLEIKEVERPTVSDGKILVKIEACGVCHTDLHAARGDWPVKPEPP 60

Query: 61  FIPGHEGVGYVSAVGSGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQ-QNTGYS 119
           FIPGHEGVG V+ VG GV+ VKEGDRVGVPWL+ ACG+C  C+ GWETLC  + Q TGY+
Sbjct: 61  FIPGHEGVGIVAEVGRGVASVKEGDRVGVPWLHHACGHCTACVTGWETLCRTEPQYTGYT 120

Query: 120 VNGGYGEYVVADPNYVGLLPDKVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGG 179
           VNGG+ EYV ADP YVG LP  + F   APILCAGVTVYKGLK  D RPGQ VVISGIGG
Sbjct: 121 VNGGFAEYVEADPAYVGHLPGALDFAPAAPILCAGVTVYKGLKECDLRPGQSVVISGIGG 180

Query: 180 LGHVAVQYARAMGLRVAAVDIDDAKLNLARRLGAEVAVNARDTDPAAWLQKEIGGAHGVL 239
           LGH+AVQYARAMGL V AVDI + KL LAR LGAE  +NA DTDP   + + +GGA GVL
Sbjct: 181 LGHLAVQYARAMGLHVIAVDIAEDKLRLARDLGAETTINAGDTDPVDEVTR-LGGADGVL 239

Query: 240 VTAVSPKAFSQAIGMVRRGGTIALNGLPPGDFGTPIFDVVLKGITIRGSIVGTRSDLQES 299
           VTAVS  AF+QA+GM+  GGT++L GLPPGDF   IFDVVL   TIRGSIVGTR+DL ES
Sbjct: 240 VTAVSNSAFTQAVGMLAPGGTMSLVGLPPGDFSLNIFDVVLNRKTIRGSIVGTRADLAES 299

Query: 300 LDFAAHGDVKATVSTAKLDDVNDVFGRLREGKVEGRVVLD 339
           L FAA G V +  +T +LD++N +F  + +GK++GR+V++
Sbjct: 300 LSFAAEGTVASHYATDRLDNINGIFEAMEQGKIDGRIVME 339


Lambda     K      H
   0.319    0.139    0.427 

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: 412
Number of extensions: 15
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: 342
Length of database: 340
Length adjustment: 29
Effective length of query: 313
Effective length of database: 311
Effective search space:    97343
Effective search space used:    97343
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: 49 (23.5 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