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_RS16735 HSERO_RS16735 alcohol dehydrogenase

Query= SwissProt::P0A388
         (468 letters)



>FitnessBrowser__HerbieS:HSERO_RS16735
          Length = 444

 Score =  439 bits (1128), Expect = e-127
 Identities = 228/428 (53%), Positives = 288/428 (67%), Gaps = 10/428 (2%)

Query: 1   MINRLKVTFSAAAFSLLAGTALAQT----PDADSALVQKGAYVARLGDCVACHTALHGQS 56
           MI    +   AA  SL A TA AQ+    P AD  LVQ+G Y+A+ GDCVACHTA  G+ 
Sbjct: 4   MIKHYFIAACAAVMSLSALTAAAQSNPAAPSADQQLVQRGEYLAKAGDCVACHTAKGGKP 63

Query: 57  YAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFS 116
           +AGGL I +PIGT+YS+NITPD   GIG Y+  +FD A+RHGIRKDG++LYPAMPYPS++
Sbjct: 64  FAGGLAIATPIGTVYSSNITPDKENGIGNYSEEDFDRALRHGIRKDGASLYPAMPYPSYA 123

Query: 117 RMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGT 176
           ++   D++ALYAYFMHGV+    P++  DI+WPLSMRWPL IWR +F+P+       P  
Sbjct: 124 KVKPADVKALYAYFMHGVQADPAPNRGVDITWPLSMRWPLSIWRKVFAPAVA--VDGPED 181

Query: 177 DPEIARGDYLVTGPGHCGACHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDP 236
           +  + RG YLV G GHCGACHTPRG  MQEKAL +     FLSGG  ID ++A +LR D 
Sbjct: 182 NSPLVRGQYLVEGLGHCGACHTPRGVGMQEKAL-SNDSSQFLSGGV-IDGYLANNLRGDG 239

Query: 237 VVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVP 296
             GLG WSE DI  FLK+GR  HSA FGGM DVVA STQY T++DL A+AKYLKSL PV 
Sbjct: 240 RDGLGNWSEADIVAFLKTGRNSHSAAFGGMADVVANSTQYMTEEDLSAMAKYLKSLKPVK 299

Query: 297 PSQGNYTYDPSTANMLASGNTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVT 356
                  YD  T   L  G+  S PGA  ++  CA CHR+ G G    FP LA +P V  
Sbjct: 300 DGTPALAYDDKTHQALRKGSDQS-PGAMAFLNNCAACHRSSGKGYDETFPSLALSPTVNA 358

Query: 357 ENPTSLVNVIAHGGVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVT 416
           ENP SL+ ++  G  +P ++ AP+  AMP +   LS Q++A+VV FIR+SWGN+A  +V+
Sbjct: 359 ENPASLIRIVLEGAEMPWTHKAPTQFAMPAFGSRLSDQEVAEVVTFIRSSWGNQA-SSVS 417

Query: 417 AADVTKLR 424
           A+DV K+R
Sbjct: 418 ASDVAKVR 425


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: 705
Number of extensions: 41
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: 444
Length adjustment: 33
Effective length of query: 435
Effective length of database: 411
Effective search space:   178785
Effective search space used:   178785
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.

Links

Downloads

Related tools

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