Alignments for a candidate for etoh-dh-c in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for etoh-dh-c in Cupriavidus basilensis 4G11

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate RR42_RS32135 RR42_RS32135 alcohol dehydrogenase

Query= BRENDA::D2SZY4
         (742 letters)



>FitnessBrowser__Cup4G11:RR42_RS32135
          Length = 733

 Score =  567 bits (1462), Expect = e-166
 Identities = 296/665 (44%), Positives = 409/665 (61%), Gaps = 33/665 (4%)

Query: 54  NWLSYGRTYSEQRYSPLDQINRSNVGDLKLAWYYTLDTNRGQEATPLVVDGIMYATTNWS 113
           +W SYG  Y+E R+S L QIN  NV DL LAW Y L++ RG EATPLVV+GIMY + +WS
Sbjct: 79  DWPSYGLDYAETRFSRLSQINADNVKDLGLAWSYDLESTRGVEATPLVVNGIMYVSASWS 138

Query: 114 KMEALDAATGKLLWQYDPKVPGNIADKGCCDTVNRGAGYWNGKVFWGTFDGRLVAADAKT 173
            + A+D  +GK +W +DPKV  +I  KGCCD VNRG   + GKVF  ++DGRL+A DA T
Sbjct: 139 VVHAIDTRSGKRIWTFDPKVDKSIGYKGCCDVVNRGVALYQGKVFVASYDGRLIALDAGT 198

Query: 174 GKKVWEVNTIPADASLGKQRSYTVDGAVRVAKGLVLIGNGGAEFGARGFVSAFDAETGKL 233
           G+K+WE +TI     + +  SYT+ GA RV KG V+IGNGGAE+G RG+++A+DA TG+ 
Sbjct: 199 GRKLWEKDTI-----IDRTHSYTITGAPRVFKGKVIIGNGGAEYGVRGYITAYDAATGEQ 253

Query: 234 KWRFYTVPNNKNEPDHAASDNILMNKAYKTWGPKGAWVRQGGGGTVWDSLVYDPVSDLIY 293
           KWR++TVP +  +P    S    M KA KTW P G +   GGGGT WD+L +DP  +L+Y
Sbjct: 254 KWRWFTVPGDPGKPFEDES----MAKAAKTWDPAGKYWEAGGGGTAWDTLAFDPELNLMY 309

Query: 294 LAVGNGSPWNYKYRSEGIGSNLFLGSIVALKPETGEYVWHFQATPMDQWDYTSVQQIMTL 353
           +  GNGSPW+   RS   G NL+L SIVAL P+TG+YVWH+Q TP D WDYTS Q ++  
Sbjct: 310 VGTGNGSPWSRSKRSPAGGDNLYLASIVALDPDTGKYVWHYQETPGDNWDYTSTQPMILA 369

Query: 354 DMPVNGEMRHVIVHAPKNGFFYVLDAKTGEFLSGKNYVYQNWANGLDPLTGRPIYNPDGL 413
           D+ + G+ R VI+HAPKNGFF+V+D   G+F+S KN+V   WA+G D   GRPI  P+  
Sbjct: 370 DLNIGGKARKVILHAPKNGFFFVIDRTNGQFISAKNFVDVTWASGYDQ-NGRPIELPEAR 428

Query: 414 YTLNGKFWYGIPGPLGAHNFMAMAYSPKTHLVYIPAHQIPFGYKNQ----VGGFKPHADS 469
            T   K +  IPGP GAHN+  M+++P+T LVY+PA  +P    +       G +P    
Sbjct: 429 AT--DKPYDAIPGPYGAHNWHPMSFNPQTGLVYLPAQHVPLNLMDDKNWTFNGKQPGQPH 486

Query: 470 WNVGLDMTKNGLPDTPEARTAYIKDLHGWLLAWDPVKMETVWKIDHKGPWNGGILATGGD 529
            NVG +  K    + P ++        G L+AWDPV+ + VW  +   PWNGG L T G+
Sbjct: 487 GNVGWNTAKFLNAEPPASKP------FGRLIAWDPVQQKAVWTQEQVSPWNGGTLTTAGN 540

Query: 530 LLFQGLANGEFHAYDATNGSDLYKFDAQSGIIAPPMTYSVNGKQYVAVEVGWGGIYPISM 589
           L+FQG A+G F AY+A  G+ L++    +G+IA P++Y V+GKQYV+V VGWGG+Y  + 
Sbjct: 541 LVFQGTADGRFIAYNAATGAKLWESPTGTGVIAAPVSYLVDGKQYVSVAVGWGGVYGQAQ 600

Query: 590 GGVGRTSGWTVNHSYIAAFSLDGKAKLPALNNRGFLPVKPPAQYDQKVVDNGYFQYQTYC 649
               R    TV       F++ GKA +PA        +    +YD   V  G   Y + C
Sbjct: 601 RATERQGPGTV-----YTFAVGGKAPMPAFVQYRAGELLSGVKYDPANVAAGTALYVSNC 655

Query: 650 QTCHGDNG-EGAGMLPDLRWAGA--IRHQDAFYNVVGRGALTAYGMDRFDTSMTPDEIEA 706
             CHG  G +  G +P+L +     I++ D F   + +G   A GM  F   ++ D++E 
Sbjct: 656 VLCHGVPGVDRGGNIPNLGYMNTAYIQNLDKF---IFKGPAMARGMPDFTGKLSADDVEK 712

Query: 707 IRQYL 711
           I+ ++
Sbjct: 713 IKAFI 717


Lambda     K      H
   0.318    0.137    0.441 

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: 2100
Number of extensions: 158
Number of successful extensions: 12
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: 742
Length of database: 733
Length adjustment: 40
Effective length of query: 702
Effective length of database: 693
Effective search space:   486486
Effective search space used:   486486
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 (21.7 bits)
S2: 55 (25.8 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