GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Methylibium petroleiphilum PM1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011830162.1 MPE_RS12990 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000015725.1:WP_011830162.1
          Length = 477

 Score =  289 bits (739), Expect = 2e-82
 Identities = 183/490 (37%), Positives = 271/490 (55%), Gaps = 33/490 (6%)

Query: 38  QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97
           + +I+  W D V  K+   VNP+T     +++ G   DVD+AVKAAR AF   + + +  
Sbjct: 6   KFYIDGHWVDPVKAKSLDVVNPATEASAGRISMGTAADVDRAVKAARKAF---ASYSQTS 62

Query: 98  ASHRGRLLNRLADLIERDRTY--LAALETLDNGKPYVISY-------LVDLDMVLKCLRY 148
            + R  LL R+  ++E  + Y  +AA  T + G P  +S        +  L + L  L+ 
Sbjct: 63  VAERASLLERI--IVEYKKRYADMAAAITEEMGAPVALSKDAQAAMGIAHLQIALDVLKN 120

Query: 149 YAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVM 208
           Y     +    T+ +          EP+GVCG I PWN+P+   A K+ PALA G  +V+
Sbjct: 121 YK--FQELRDTTLMVK---------EPIGVCGFITPWNWPVNQIACKVAPALAVGCTMVL 169

Query: 209 KVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGR 268
           K +E  P +A     ++  AG P GV N+V G GPT GAA++SH DVD V+FTGST  G 
Sbjct: 170 KPSEIAPFSAYLWTEILHAAGVPAGVFNLVNGDGPTVGAALSSHPDVDMVSFTGSTRAG- 228

Query: 269 VIQVAAGSS-NLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFV 327
            ++VA  ++  +KRV  ELGGKSPNII+ DAD   A+      +  N GQ C A +R  V
Sbjct: 229 -VEVARNAAPTVKRVHQELGGKSPNIILPDADFKHAITAGVQGVMLNSGQSCNAPTRMLV 287

Query: 328 QEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCG 387
                DE +  +   A++  VG+P  S    GP +  TQ+ KI   I+ G +EGA ++ G
Sbjct: 288 PNARLDEALAIAKEAAEATTVGDP-ASGAALGPVISATQWDKIQTLIHKGIEEGATVVAG 346

Query: 388 G---GIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGL 444
           G       + GY+++PTV G V + MT+A+EEIFGPV+ IL + T+++ V   N++ YGL
Sbjct: 347 GPGKPKGLETGYYVKPTVLGHVNNQMTVAREEIFGPVLTILGYDTVDQAVEIGNDTPYGL 406

Query: 445 AAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTE 504
           AA V   D +    ++  L+AG V +N   +   ++PFGG+K SG+GRE G++    + E
Sbjct: 407 AAYVSGTDPEATRKVASRLRAGQVNINSVPL-DFKAPFGGFKQSGNGREWGDHAFGEFLE 465

Query: 505 VKTVTVKVPQ 514
           VK V    P+
Sbjct: 466 VKAVLGYAPK 475


Lambda     K      H
   0.319    0.136    0.409 

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: 585
Number of extensions: 27
Number of successful extensions: 6
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: 517
Length of database: 477
Length adjustment: 34
Effective length of query: 483
Effective length of database: 443
Effective search space:   213969
Effective search space used:   213969
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: 52 (24.6 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