GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Rhodococcus qingshengii djl-6-2

Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_003942060.1 C1M55_RS09025 iron-containing alcohol dehydrogenase

Query= BRENDA::A0A0H3W5U9
         (873 letters)



>NCBI__GCF_002893965.1:WP_003942060.1
          Length = 401

 Score =  179 bits (454), Expect = 3e-49
 Identities = 128/437 (29%), Positives = 216/437 (49%), Gaps = 42/437 (9%)

Query: 434 SVSDNVGVKHLLNIKTVAERRENMLWFRTPEKIYIKRGCLPVALDELKNVMGKKKAFIVT 493
           SV+    V H ++ +  A R   ++ F  PE ++     +  A   L+   G  + F+VT
Sbjct: 2   SVAYPDAVNHGVHRRGTAAR---LVKFHAPEIVFGIGSLVEAAHATLR--FGGFRPFLVT 56

Query: 494 DNFLYNNGYTKPITDKLDEMGIVHKTFFDVSPDPSLASAKAGAAEMLAFQPDTIIAVGGG 553
           D  L + G+   + D L E G+    +  ++P+P      AG       + D IIA+GGG
Sbjct: 57  DPGLIDAGWVSELEDHLTEQGLTATVWSGLTPNPKDFEIAAGFEVYQEGECDVIIALGGG 116

Query: 554 SAMDAAKIMWVMYEHPEVDFMDMAMRFMDIRKRVYTFPKMGQKAYFIAIPTSAGTGSEVT 613
           S +DAAK + V+  +   + +D    +  + +     P +      + +PT++GTG++V+
Sbjct: 117 SVIDAAKGVAVLAANGG-NILD----YEGVDQATKPIPPL------VMVPTTSGTGADVS 165

Query: 614 PFAVITDEKTGIKYPLADYELLPDMAIVDADMMMNAPKGLTAASGIDALTHALEAYVSML 673
            F ++TD   G K  +    L+PD+ ++D  ++   P+ L AA+G+DALTH +EA+VS+ 
Sbjct: 166 QFCIVTDTTRGTKITIIGRALVPDVTVIDPRLLTTMPEWLNAATGLDALTHGIEAFVSLA 225

Query: 674 ATDYTDSLALRAIKMIFEYLPRAYENGASDPVAREKMANAATIAGMAFANAFLGVCHSMA 733
               TD  ALRA+ ++ E L    ++   +  AR  MA A+  AG+AF NA LG  H+M+
Sbjct: 226 HNPLTDHHALRAVGLVTENLVHTIQD-PMEMEARSVMAQASLEAGLAFTNAILGAAHAMS 284

Query: 734 HKLGAFYHLPHGVANALMINEVIRFNSS--EAPTKMGTFPQYDHPRTLERYAEIADYIGL 791
           H++G    LPHGV N +++  VIRFNS+   AP                 +  IA  + L
Sbjct: 285 HQVGGMLDLPHGVINGILLPHVIRFNSTTDAAP-----------------FVAIAAALSL 327

Query: 792 KGKNN--EEKVENLIKAIDELKEKVGIRKTIKDYDIDEKEFLDRLDEMVEQAFDDQCTGT 849
             +    EE    +   ++ L  +VG+ K + +  + E++    L  +   A  D C  T
Sbjct: 328 PEQRGTPEEAALAVADRVERLAREVGVPKGLGELGVREED----LSRLASFALLDACMST 383

Query: 850 NPRYPLMNEIRQMYLNA 866
           NPR     ++  ++  A
Sbjct: 384 NPREATQEQMVALFRGA 400


Lambda     K      H
   0.318    0.134    0.382 

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: 768
Number of extensions: 38
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 873
Length of database: 401
Length adjustment: 37
Effective length of query: 836
Effective length of database: 364
Effective search space:   304304
Effective search space used:   304304
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: 53 (25.0 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