GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Amycolatopsis halophila YIM 93223

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  389 bits (999), Expect = e-112
 Identities = 214/477 (44%), Positives = 286/477 (59%), Gaps = 9/477 (1%)

Query: 38  QIFINNEWHDAVSRKTFPTV-NPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRM 96
           ++FI+  W D         V NP+    +  V E D++DVD AV AAR AF   SPWR  
Sbjct: 3   ELFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFD-DSPWRAT 61

Query: 97  DASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKY 156
            A  RG LL  +A L++RD+ +LA  E+LD GK  +    VD+D V    RYYA  AD  
Sbjct: 62  TARERGELLREIARLLQRDKEHLARTESLDTGKT-MAEGRVDVDDVTSVFRYYANLADNE 120

Query: 157 HGKTIPI-DGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTP 215
            G+ +   D    S   HEPVGVC  I PWN+PLL  +WKL PALA GN VVMK +E TP
Sbjct: 121 AGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTP 180

Query: 216 LTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAG 275
           LT + +  L++EAG P GVVN+V G G   GA + SH DVD V+FTG  E G+ I +A  
Sbjct: 181 LTTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKI-MAMA 239

Query: 276 SSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEF 335
           +  +KRV LELGGK+PN++ +DAD D AV+ A  A F + GQ C AGSR  V+ DI+DEF
Sbjct: 240 AEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEF 299

Query: 336 VERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD-- 393
           V     RA +  +G+  D  TE GP        K+  +I   K EGA+L+ GG    +  
Sbjct: 300 VAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPE 359

Query: 394 --RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTK 451
              GYF++PTVF D    M I ++E+FGPV+ + +F T +E +  AN++ YGLA AV+T 
Sbjct: 360 LADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTS 419

Query: 452 DLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508
           D  +A  ++ AL+ GTVW+N +  +  Q+ +GG+  SG GRELG  GL+ Y E K +
Sbjct: 420 DASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476


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: 662
Number of extensions: 29
Number of successful extensions: 5
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: 496
Length adjustment: 34
Effective length of query: 483
Effective length of database: 462
Effective search space:   223146
Effective search space used:   223146
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