Alignments for a candidate for adhAqn in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for adhAqn in Marinobacter adhaerens HP15

Align Alcohol dehydrogenase (quinone), dehydrogenase subunit; ADH; Alcohol dehydrogenase (quinone), acceptor subunit; Alcohol dehydrogenase (quinone), subunit I; Ethanol:Q2 reductase; G3-ADH subunit I; Quinohemoprotein alcohol dehydrogenase; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate GFF3222 HP15_3164 quinoprotein alcohol dehydrogenase

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__Marino:GFF3222
          Length = 617

 Score =  294 bits (752), Expect = 1e-83
 Identities = 211/619 (34%), Positives = 306/619 (49%), Gaps = 64/619 (10%)

Query: 9   IKVTKKRLL-SCAAALAFSAAVPVA---FAQEDTGTAITSSDNGGHPGDWLSYGRSYSEQ 64
           IK  K  LL     ALA S+A  +A    A++ T   I  +++   P + L YG     Q
Sbjct: 3   IKTRKHPLLRGIGLALALSSAAGLASQVHAKDVTWDDI--ANDAQTPENVLGYGIGPKAQ 60

Query: 65  RYSPLDQINTENVGKLKLAWHYDL--DTNRGQEGTPLIVNGVMYATTNWSKMKALDAATG 122
           RYSP+  IN +NV +L  AW +    +  RGQE   L+ +GV+Y T ++S++ ALDA TG
Sbjct: 61  RYSPMTTINRDNVERLVPAWSFSFGDEKQRGQESQALVHDGVVYVTGSYSRLFALDAKTG 120

Query: 123 KLLWSYDPKVPGNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVYTI 182
           + LW Y  ++P  I  R CCD V+RGAA +  KV+FGT D  ++AL+  TGK+VW     
Sbjct: 121 ERLWEYSHRLPEGI--RPCCDVVNRGAAIFGDKVFFGTLDAGIVALNKDTGKVVW----- 173

Query: 183 PKEAQLGHQRSYTVDGAPRIAKG-KVLIGNGGA-----EFGARGFVSAFDAETGKLDWRF 236
            +E    H+  YT+ GAP + K  K   G   +     EFG  G + A D +TGK  W  
Sbjct: 174 -REKFADHEAGYTMTGAPTLVKDQKNRQGTADSRLLRDEFGVVGKLFARDPDTGKEIWMR 232

Query: 237 FTVPNPENKPDGAASDDILMSKAYPTW--------GKNGAWKQQGGGGTVWDSLVYDPVT 288
             V     + +G  S      +A P+W        GK  AW    GGG  W S  +D  T
Sbjct: 233 PFVEGHYGRLNGEKSTPTGDPRA-PSWPDDPNTETGKVEAWSH--GGGAPWQSASFDAET 289

Query: 289 DLVYLGVGNGSPWNYKFRSEGKGD-----NLFLGSIVAINPDTGKYVWHFQETPMDEWDY 343
           + + +G GN +PWN   R+   GD     NL+    V ++P TG+  W +Q TP D WD+
Sbjct: 290 NTIIIGAGNPAPWNTWKRTSPGGDPADYDNLYTSGQVGVDPTTGEVKWFYQHTPNDAWDF 349

Query: 344 TSVQQIMTLDMPVNGEMRHVIVHAPKNGFFYIIDAKTGKFITGKPYTYE-NWANGLDPVT 402
           +   +++  +   NGE      HA +NGFFY++D + G+F  G P+     WA  +    
Sbjct: 350 SGNNELVLFEYDENGETVKATAHADRNGFFYVVDRENGEFKKGFPFVDNITWAERIGD-D 408

Query: 403 GRP------NYVPDALWTLTGKPWLGIPGELGGHNFAAMAYSPKTKLVYIPAQQIPLLYD 456
           GRP         P A     G+     P  LGG N+  MAYS  T L Y+PA      Y 
Sbjct: 409 GRPVERKGQRPPPVAQGETRGEAIEVSPPFLGGKNWNPMAYSQDTGLFYVPANHWKEDYW 468

Query: 457 GQKGGFKAYHDAWNLGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGWTVAWDPEKMAPAFT 516
            ++  +K    A  LG       ++DD    HV   +  +  L G  + W+ ++  P + 
Sbjct: 469 TEEVTYK--KGAAYLGQGFRIKRMYDD----HVGILR-AMNPLTG-EIEWEHKERLPLW- 519

Query: 517 INHKGPWNGGLLATAGNVIFQGLANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYTANGK 576
                    G+L T G ++F G  +G   A+DA  G +L+ F   S II+ P+T+  +G+
Sbjct: 520 --------AGVLTTKGGLVFTGTGDGFLKAFDAETGEELWKFQTGSGIISSPITWEMDGE 571

Query: 577 QYVAVEVGWGGIYPFLYGG 595
           QY+ V  G+GG  P L+GG
Sbjct: 572 QYIGVASGYGGAVP-LWGG 589


Lambda     K      H
   0.317    0.136    0.435 

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: 1865
Number of extensions: 160
Number of successful extensions: 19
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 757
Length of database: 617
Length adjustment: 39
Effective length of query: 718
Effective length of database: 578
Effective search space:   415004
Effective search space used:   415004
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: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources