GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adhBqn in Herbaspirillum seropedicae SmR1

Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate HSERO_RS22390 HSERO_RS22390 alcohol dehydrogenase

Query= SwissProt::P0A388
         (468 letters)



>FitnessBrowser__HerbieS:HSERO_RS22390
          Length = 466

 Score =  428 bits (1100), Expect = e-124
 Identities = 213/420 (50%), Positives = 280/420 (66%), Gaps = 9/420 (2%)

Query: 18  AGTALAQ------TPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIY 71
           A TALAQ      +  A+   + +GAY+AR GDCVACHT+  G  +AGGL + SPIG IY
Sbjct: 46  ADTALAQRIAAQGSASAEDQQILRGAYLARAGDCVACHTSKGGAPFAGGLALASPIGAIY 105

Query: 72  STNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFM 131
           STNITPD  +GIG +++ +F   +R G+ K G T+YPAMPYPS+SR+T EDMQALYAYF 
Sbjct: 106 STNITPDKQHGIGDWSYEDFARLMRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFS 165

Query: 132 HGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPG 191
             V P AQ ++  DI WPLSMRWPL +WR +F+P+P  +TPA G+D E+ARG YLV G G
Sbjct: 166 KAVPPSAQENRANDIPWPLSMRWPLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLG 225

Query: 192 HCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTF 251
           HCG+CH+PR   MQEKAL   GG  FLSGG  +D W  PSLRN+   G+  WS+ D+  F
Sbjct: 226 HCGSCHSPRAVTMQEKALKEDGGRLFLSGGQVVDGWSVPSLRNEHGGGIAGWSQADLVEF 285

Query: 252 LKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANM 311
           L++GR  ++A FG M DV+  S QY +D DL+A+A+YL SLPP       Y YD +TA  
Sbjct: 286 LRTGRNQYTASFGAMNDVIEDSMQYMSDADLNAMARYLLSLPP-RQQAAPYRYDSATAQA 344

Query: 312 LASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGV 371
              G     PGA  Y+  CA CHR++G G  + FP LAGNPV+ T + TS + +I  GG 
Sbjct: 345 AYDGRPDG-PGARIYLDRCAACHRSNGTGYGKAFPALAGNPVLQTSDATSAIRIILQGGR 403

Query: 372 LPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLRDTGAPVS 431
            P +  A + + M  Y++ L  QQ+A+V ++I+T+WGN+  GT TAA+V K+R T  PV+
Sbjct: 404 QPSTASATAGLVMAPYAQLLDDQQVAEVTSYIQTAWGNRG-GTTTAAEVAKVRKTAVPVA 462


Lambda     K      H
   0.317    0.134    0.425 

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: 792
Number of extensions: 50
Number of successful extensions: 6
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: 468
Length of database: 466
Length adjustment: 33
Effective length of query: 435
Effective length of database: 433
Effective search space:   188355
Effective search space used:   188355
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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