GapMind for catabolism of small carbon sources

 

Aligments 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_RS22810 HSERO_RS22810 alcohol dehydrogenase

Query= SwissProt::P0A388
         (468 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22810 HSERO_RS22810 alcohol
           dehydrogenase
          Length = 423

 Score =  342 bits (876), Expect = 2e-98
 Identities = 192/426 (45%), Positives = 257/426 (60%), Gaps = 13/426 (3%)

Query: 2   INRLKVTFSAAAFSLLAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGL 61
           + +L   F+A A+SL A   L     AD  LV +G Y+AR GDC+ACH+A    +Y+GGL
Sbjct: 1   MKKLTSLFAALAWSLGALGTLTTAQAADQDLVARGQYLARAGDCMACHSAAGKPAYSGGL 60

Query: 62  EIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKE 121
            I S  G IYSTNITPD  +GIG Y+ A+F  AVRHG+R DG+ LYPAMPYPS+++++ E
Sbjct: 61  AIDSGHGIIYSTNITPDKEHGIGNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDE 120

Query: 122 DMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIA 181
           D+ ALY YFM GV+PVA       +S+P ++RW + +W + F+ + K F    G   EI 
Sbjct: 121 DIHALYTYFMQGVQPVASTPPASSMSFPFNIRWGMKLWNVFFA-NDKPFREQDGWSAEIK 179

Query: 182 RGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLG 241
           RG YLV G GHCG+CHTPRG AM EKA D++    FLSGG  ++ W  PSLR     G+ 
Sbjct: 180 RGAYLVEGLGHCGSCHTPRGVAMNEKASDSSQA-QFLSGG-DLNGWAVPSLR-----GMP 232

Query: 242 RWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGN 301
            WS  DI  +L++GR   ++V G M  VV  ST +   +DL A+A YLK+L PV  S G+
Sbjct: 233 HWSAQDIVDYLQTGRNKTASVAGEMSLVVEHSTSHLKREDLQAMAAYLKTLSPV-ASSGS 291

Query: 302 YTYDPSTANMLASGNTAS---VPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTEN 358
               P   +   S  TA+     G   Y+  CA CH   G G   +FP L G  VV  EN
Sbjct: 292 GRVIPQGVDATVSKLTAAKDLTLGERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAEN 351

Query: 359 PTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAA 418
           P++L++VI  G   P +  APS + MPG++  LS ++ A +  F+R  WGN A G V+  
Sbjct: 352 PSALLHVILAGARTPSTEKAPSILVMPGFAHRLSDEEAAALATFVRQGWGNHA-GKVSER 410

Query: 419 DVTKLR 424
           +V KLR
Sbjct: 411 EVGKLR 416


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: 622
Number of extensions: 37
Number of successful extensions: 7
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: 423
Length adjustment: 32
Effective length of query: 436
Effective length of database: 391
Effective search space:   170476
Effective search space used:   170476
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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