GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Jannaschia aquimarina GSW-M26

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_043919199.1 jaqu_RS11825 NADH-quinone oxidoreductase subunit NuoF

Query= uniprot:Q39TW5
         (635 letters)



>NCBI__GCF_000877395.1:WP_043919199.1
          Length = 432

 Score =  285 bits (730), Expect = 2e-81
 Identities = 154/393 (39%), Positives = 238/393 (60%), Gaps = 10/393 (2%)

Query: 164 SKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW----EESRNAPDPIKYVIVNADEGD 219
           +K L  +  + ++  +K S LRGRGG GFP   KW    +ES   P    Y++VNADE +
Sbjct: 32  TKDLIGLGRDKIVQIMKDSGLRGRGGAGFPTGLKWSFMPKESDGRP---AYLVVNADESE 88

Query: 220 PGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGF 279
           PG   DR ++  +PH+++EG +I ++A+GAH  +IY+R EY    E +  AI +A + G 
Sbjct: 89  PGTCKDREIMRHDPHTLIEGCLIASFAMGAHACYIYIRGEYIREKEALQNAIDEAYDAGL 148

Query: 280 VGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSV 339
           +G++  GSG+DF + +H GAGA++CGE +AL+ +LEG+ G PR K    A  G++  P+ 
Sbjct: 149 IGRNACGSGWDFDLYLHHGAGAYICGEETALIESLEGKKGMPRMKPPFPAGAGLYGCPTT 208

Query: 340 LNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIIT 399
           +NNVE+ A V  I+ +GA+WF  +G   + GTK+F++ G +    +VE  M +  +++I 
Sbjct: 209 VNNVESIAVVPTILRRGAEWFAQFGRPNNAGTKLFAISGHVNRPCVVEEAMSIPFQELID 268

Query: 400 KVGGGIPGG-KKFKAVQTGGPSGGCIP-EAMLDLPVDFDELTKAGSMMGSGGMIVMDEDT 457
           K  GGI GG    KA+  GG S   +P E   +  +DFD L +  S +G+  +IVMDE T
Sbjct: 269 KHCGGIRGGWDNLKAIIPGGSSVPLLPREIAREAIMDFDWLREQKSGLGTAAVIVMDEST 328

Query: 458 CMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEELAEST-G 516
            ++        F K ESCG+CTPCREG   M+ V+ R+  G+ +  +I++L ++ +   G
Sbjct: 329 DIIKAIWRLSAFYKHESCGQCTPCREGTGWMMRVMDRLVKGEAEVEEIDMLLDVTKQVEG 388

Query: 517 AALCALGKSAPNPVLSTIRYFRDEYEAHIREKK 549
             +CALG +A  P+   IR+FRDE E  I+ K+
Sbjct: 389 HTICALGDAAAWPIQGLIRHFRDEIEDRIKAKR 421


Lambda     K      H
   0.319    0.138    0.420 

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: 741
Number of extensions: 38
Number of successful extensions: 4
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: 635
Length of database: 432
Length adjustment: 35
Effective length of query: 600
Effective length of database: 397
Effective search space:   238200
Effective search space used:   238200
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