GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Paenisporosarcina indica PN2

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_075620503.1 GY23_RS17650 iron-containing alcohol dehydrogenase

Query= BRENDA::A4ISB9
         (387 letters)



>NCBI__GCF_001939075.1:WP_075620503.1
          Length = 387

 Score =  562 bits (1449), Expect = e-165
 Identities = 263/387 (67%), Positives = 325/387 (83%)

Query: 1   MQNFTFRNPTKLIFGRGQIEQLKEEVPKYGKKVLLVYGGGSIKRNGLYDEVMSLLTDIGA 60
           M  F+F NP KLIFG+GQ+E++K+E+P YG+KVL+VYGGGSIK+NGLYDEVM +L +   
Sbjct: 1   MNAFSFYNPVKLIFGKGQLEEIKQELPIYGQKVLVVYGGGSIKKNGLYDEVMDVLKEANL 60

Query: 61  EVVELPGVEPNPRLSTVKKGVDICRREGIEFLLAVGGGSVIDCTKAIAAGAKFDGDPWEF 120
           EV EL GVEPNPR+STV++GV++C++E IE LLAVGGGSVIDCTK I+AGA +DGD W+F
Sbjct: 61  EVFELSGVEPNPRISTVRRGVELCKQENIEMLLAVGGGSVIDCTKLISAGALYDGDAWDF 120

Query: 121 ITKKATVTEALPFGTVLTLAATGSEMNAGSVITNWETKEKYGWGSPVTFPQFSILDPTYT 180
           +++KAT   ALPFGTVLTLAATGSEMN+GSVITN ET+EKYGWG+P+ FP+FS+LDPTYT
Sbjct: 121 VSRKATPKAALPFGTVLTLAATGSEMNSGSVITNEETQEKYGWGTPLVFPKFSVLDPTYT 180

Query: 181 MTVPKDHTVYGIVDMMSHVFEQYFHHTPNTPLQDRMCEAVLKTVIEAAPKLVDDLENYEL 240
            +VP D TVYGIVDMMSH+FEQYF++  NTP+QD MCE VL+ ++E APKL+ DL +YE 
Sbjct: 181 FSVPLDQTVYGIVDMMSHIFEQYFNNATNTPVQDEMCEGVLRAIMETAPKLLKDLHSYEH 240

Query: 241 RETIMYSGTIALNGFLQMGVRGDWATHDIEHAVSAVYDIPHAGGLAILFPNWMKHVLDEN 300
           RETI+++GT+ LN FLQMG RGDWATH+IEHAVSAVYDIPHAGGLAILFP+WM+H +  N
Sbjct: 241 RETILFAGTMGLNNFLQMGYRGDWATHNIEHAVSAVYDIPHAGGLAILFPHWMRHNVKVN 300

Query: 301 VSRFAQLAVRVFDVDPTGKTERDVALEGIERLRAFWSSLGAPSRLADYGIGEENLELMAD 360
             RFA+LAV VF V+P GKT  ++ALEGI+ LRA+W+SLGAP  LADY I + N+ELM +
Sbjct: 301 PERFARLAVYVFGVEPDGKTVEEIALEGIDNLRAYWTSLGAPQTLADYNIDDSNIELMVE 360

Query: 361 KAMAFGEFGRFKTLNRDDVLAILRASL 387
           KAM +G FG F  L  +DV AIL+ASL
Sbjct: 361 KAMVYGPFGNFTALQAEDVRAILKASL 387


Lambda     K      H
   0.320    0.138    0.412 

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: 582
Number of extensions: 21
Number of successful extensions: 1
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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:

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