GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamH in Xanthobacter autotrophicus Py2

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate WP_012116598.1 XAUT_RS23440 NADH-quinone oxidoreductase subunit NuoF

Query= uniprot:Q39TW5
         (635 letters)



>NCBI__GCF_000017645.1:WP_012116598.1
          Length = 433

 Score =  273 bits (697), Expect = 1e-77
 Identities = 150/389 (38%), Positives = 226/389 (58%), Gaps = 11/389 (2%)

Query: 164 SKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKW----EESRNAPDPIKYVIVNADEGD 219
           +K + +   + ++ E+K S LRGRGG GF    KW    ++S   P    Y++VNADE +
Sbjct: 32  TKAILEKGRDWIINEMKTSGLRGRGGAGFSTGMKWSFMPKQSDGRPH---YLVVNADESE 88

Query: 220 PGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQASERGF 279
           PG   DR ++  +PH+++EG +I ++A+GAH  +IYVR EY    + +  AI +A + G 
Sbjct: 89  PGTCKDREIMRNDPHTLIEGCLIASFAMGAHAAYIYVRGEYIFERKRLQAAIDEAYDAGL 148

Query: 280 VGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVWDHPSV 339
           +GK  +   + F + VH GAGA++CGE +AL+ +LEG+ G PR K    A  G++  P+ 
Sbjct: 149 IGKSNIHD-YPFDLYVHHGAGAYICGEETALLESLEGKKGMPRLKPPFPANMGLYGCPTT 207

Query: 340 LNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTLRDIIT 399
           +NNVE+ A    I+ +GA WF+S G   + GTK+FSL G +    +VE  M +  R+++ 
Sbjct: 208 VNNVESIAVAPTILRRGAAWFSSIGRPNNVGTKLFSLAGHVNTPCVVEEAMSIPFRELVD 267

Query: 400 KVGGGIPGG-KKFKAVQTGGPSGGCIP-EAMLDLPVDFDELTKAGSMMGSGGMIVMDEDT 457
           K GGG+ GG      +  GG S   IP E   DL +DFD      S +G+ G++VMD+ T
Sbjct: 268 KHGGGVRGGWDNLLGIIPGGASCPVIPAEQCADLIMDFDGTRAVKSSLGTAGVLVMDKST 327

Query: 458 CMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE-LLEELAESTG 516
            ++        F K ESCG+CTPCREG   M  V+ R+  G+ ++ +I+ LLE   +  G
Sbjct: 328 DIIKAIARISAFFKHESCGQCTPCREGTGWMWRVVNRMAEGRAQKREIDMLLEVTTQIEG 387

Query: 517 AALCALGKSAPNPVLSTIRYFRDEYEAHI 545
             +CALG +A  PV   IR++R   E  I
Sbjct: 388 HTICALGDAAAWPVQGLIRHYRHVIEERI 416


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: 759
Number of extensions: 45
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: 635
Length of database: 433
Length adjustment: 35
Effective length of query: 600
Effective length of database: 398
Effective search space:   238800
Effective search space used:   238800
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 Apr 09 2024. 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