GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adhAqn in Sinorhizobium meliloti 1021

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 SM_b20173 SM_b20173 methanol dehydrogenase, large subunit

Query= SwissProt::O05542
         (757 letters)



>FitnessBrowser__Smeli:SM_b20173
          Length = 601

 Score =  308 bits (789), Expect = 5e-88
 Identities = 211/613 (34%), Positives = 301/613 (49%), Gaps = 68/613 (11%)

Query: 14  KRLLSCAAALAFSAAVPVAFAQEDTGTAITSSDNGGHPGDWLSYGRSYSEQRYSPLDQIN 73
           KRLL+  A ++      VAFA ++    I        P  W      Y+  RYS LDQIN
Sbjct: 2   KRLLTMLAIMSIGGGAQVAFANDELQKLIDD------PNQWAIQTGDYANLRYSKLDQIN 55

Query: 74  TENVGKLKLAWHYDLDTNRGQEGTPLIVNGVMYATTNW-SKMKALDAAT-GKLLWSYDPK 131
            +NVGKL++AW +     RG EG+PL++  +MY  T + + + ALD +  G+++W Y+PK
Sbjct: 56  KDNVGKLQVAWTFSTGVLRGHEGSPLVIGDLMYVHTPFPNTVYALDLSKDGQIVWKYEPK 115

Query: 132 VPGNIADRGCCDTVSRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVYTIPKEAQLGHQ 191
              N+    CCDTV+RG AY + K++    D  ++ALDAKTGK++WSV     +A  G  
Sbjct: 116 QDPNVIPVMCCDTVNRGVAYADNKIFLHQADTTVVALDAKTGKVIWSVKN--GDATKGET 173

Query: 192 RSYTVDGAPRIAKGKVLIGNGGAEFGARGFVSAFDAETGKLDWRFF-------TVPNPE- 243
            + TV       K K+L+G  G EFG RG V+A+    GK+ WR +       T+ +PE 
Sbjct: 174 NTATV----MPVKDKILVGISGGEFGVRGHVTAYSMADGKVLWRGYSMGPDSDTLIDPEK 229

Query: 244 ----NKPDGAASDDILMSKAYPTWGKNGAWKQQGGGGTVWDSLVYDPVTDLVYLGVGNGS 299
                KP G  S          TW +   WK   GGGT W    YDP  +LVY G GN S
Sbjct: 230 TTHLGKPVGKDS-------GLTTW-EGDQWKI--GGGTTWGWYSYDPEENLVYYGTGNPS 279

Query: 300 PWNYKFRSEGKGDNLFLGSIVAINPDTGKYVWHFQETPMDEWDYTSVQQIMTLDMPVNGE 359
            WN    ++  GDN +  +I A + DTG   W +Q TP DEWDY  V +++  +  ++G+
Sbjct: 280 TWN---PTQRPGDNRWSMTIFARDVDTGMAKWLYQMTPHDEWDYDGVNEMILTEQQIDGK 336

Query: 360 MRHVIVHAPKNGFFYIIDAKTGKFITGKPY-TYENWANG--LDPVT---GRPNYVPDALW 413
            R ++ H  +NGF Y +D  TG+ +  + Y    NWA    +DP +   GRP  V     
Sbjct: 337 DRKLLTHFDRNGFGYTMDRVTGELLVAEKYDPTVNWATEVVMDPKSDKYGRPQVVAQYST 396

Query: 414 TLTGKP--WLGI-PGELGGHNFAAMAYSPKTKLVYIPAQQIPLLYDGQKGGFKAYHDAWN 470
              G+     G+ P  LG  +    AYSPKT+L Y+P   + + Y+  +  + A      
Sbjct: 397 EQNGEDTNTTGVCPAALGTKDQQPAAYSPKTELFYVPTNHVCMDYEPFRVSYTAGQPYVG 456

Query: 471 LGLDMNKIGLFDDNDPEHVAAKKDFLKVLKGWTVAWDPEKMAPAFTINHKGPWNGGLLAT 530
             L M     +   D               G  +AWD ++    +++        G LAT
Sbjct: 457 ATLSM-----YPPKDSHGG----------MGNFIAWDNKEGKIKWSLPEPFSVWSGALAT 501

Query: 531 AGNVIFQGLANGEFHAYDATNGNDLYSFPAQSAIIAPPVTYTANGKQYVAVEVGWGGIYP 590
           AG+V+F G   G   A DA  G +LY F   S +I   +TY   GKQYVAV  G GG   
Sbjct: 502 AGDVVFYGTLEGYLKAVDAATGKELYRFKTPSGVIGNVMTYAREGKQYVAVLSGVGG--- 558

Query: 591 FLYGGVARTSGWT 603
             + G+   +G T
Sbjct: 559 --WAGIGLAAGLT 569


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: 1781
Number of extensions: 137
Number of successful extensions: 15
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 4
Length of query: 757
Length of database: 601
Length adjustment: 39
Effective length of query: 718
Effective length of database: 562
Effective search space:   403516
Effective search space used:   403516
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.

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