GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Marinicella litoralis KMM 3900

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_099017984.1 CCS90_RS02830 3-hydroxybutyrate dehydrogenase

Query= BRENDA::Q4J702
         (264 letters)



>NCBI__GCF_002591915.1:WP_099017984.1
          Length = 254

 Score =  118 bits (295), Expect = 1e-31
 Identities = 84/261 (32%), Positives = 124/261 (47%), Gaps = 22/261 (8%)

Query: 9   VKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGHEVNHMK-- 66
           +K M   + GASSGIGK IA+  +    +V++SD     +K+    L+ +G  V      
Sbjct: 1   MKPMRVFITGASSGIGKGIAQHLAP-DHEVIISDCSAAAIKQAQQDLKRQGCHVEAQVFD 59

Query: 67  -CDITDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKSIENYTYEDFEKVINVNLKGNFM 125
            CD TDL Q++K+ + +      +D L     I   K +E +  E ++++INV L G  M
Sbjct: 60  VCDATDLAQLRKMADEN-----RIDVLINNAGIQYVKPLEEFPPEKWQQLINVMLVGPAM 114

Query: 126 VVKEFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEYGKYNIR 185
             +  L  MK N  G  ++   S+   V    +S Y   K G++ LAK  A E    NI 
Sbjct: 115 TTRAVLPAMKANNFG-RIINIGSVHSLVASAYKSAYVAAKHGLLGLAKTVALEVAAANIT 173

Query: 186 VNVIAPGVVDTPLTR-QIKSDPEWFKAYTEKTIL----------KRWATPEEIANVALFL 234
           +N + PG VDT + R QIK   E  +   E T++          K +    E+A    FL
Sbjct: 174 INTLCPGYVDTDMVRDQIKQQAEAHQ-IPESTVINDIMLKSMPKKEFIEISELAGTVAFL 232

Query: 235 AMPASSYITGTVIYVDGGWTA 255
             P +  IT   I +DGGWTA
Sbjct: 233 MGPYAKNITAQAITLDGGWTA 253


Lambda     K      H
   0.317    0.134    0.381 

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: 135
Number of extensions: 10
Number of successful extensions: 4
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: 264
Length of database: 254
Length adjustment: 24
Effective length of query: 240
Effective length of database: 230
Effective search space:    55200
Effective search space used:    55200
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: 47 (22.7 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