Alignments for a candidate for patD in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for patD in Nocardioides daejeonensis MJ31

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_110207793.1 DNK54_RS15005 aldehyde dehydrogenase

Query= BRENDA::C0P9J6
         (505 letters)



>NCBI__GCF_003194585.1:WP_110207793.1
          Length = 501

 Score =  352 bits (904), Expect = e-101
 Identities = 201/485 (41%), Positives = 283/485 (58%), Gaps = 9/485 (1%)

Query: 7   VPLRQLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGR 66
           VP  Q F++G W     G+ L V +P T   +  +  G A ++DAAVAAA+AA   +   
Sbjct: 3   VPHYQNFINGAWTD--NGQVLEVRSPATGELVATVAKGGAAEIDAAVAAAKAA---HAAG 57

Query: 67  DWARAPGAVRAKYLRAIAAKVIERKPELAKLEALDCGKPYD-EAAWDMDDVAGCFEYFAD 125
            W   P A RA  + A+A  +  R  ELA L++ + G       A  +       ++ A 
Sbjct: 58  VWRNTPPAERAALINAVAGDLAGRLEELAALQSRENGATIRVTGALHVGLSIANMQFIAA 117

Query: 126 QAEALDKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKIAPALAAGCTAV 185
           QA   +  +  P   P+   +  LRREP+GVVG I PWN PLL   WK+ PALAAG T V
Sbjct: 118 QAAEYEFEKAGPEIGPVPA-EGILRREPLGVVGAIVPWNIPLLTIVWKVTPALAAGNTVV 176

Query: 186 LKPSELASVTCLELADICKEVGLPSGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETG 245
           LKP E A +  LELA   +  GLP+GVLN+V G G DAGA LS HPDV K+ FTGS E G
Sbjct: 177 LKPDEHAPLLALELAKAFEAAGLPAGVLNVVVGEGHDAGARLSQHPDVRKIGFTGSTEVG 236

Query: 246 KKIMASAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLIH 305
           K I+ ++A  +K VTLELGGK P ++ DD D+D A++  ++ C   NG+ C A +RLL+ 
Sbjct: 237 KSILGASADNMKRVTLELGGKGPNILLDDADLDVAIDGAIYACMANNGEACEAGTRLLVP 296

Query: 306 TKIAKKFNERMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGG 365
                +  ER+VA    +K+ +PL+    +GP+++  Q +++   I+ A++QGA +  GG
Sbjct: 297 NSRKDEIVERLVARVGTMKIGNPLDPATDIGPLITADQRDRVLAHIAKAETQGAKVAIGG 356

Query: 366 VRPAHLE--KGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGL 423
             PA  E   G+F+EPT++TD+T SM +  EEVFGPVL V  + T DEAI +ANDT+YGL
Sbjct: 357 SAPAGEEFANGYFVEPTVLTDVTPSMTVACEEVFGPVLSVLGYDTVDEAIAIANDTEYGL 416

Query: 424 AGAVISGDRERCQRLSEEIDAGCIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLS 483
           +  V   D  R   ++ +++AG I+VN         P+GG K+SG GRE G   +D Y  
Sbjct: 417 SAGVWGTDETRVLDVARQLEAGMIYVNDWHVLHPAYPFGGYKQSGLGREGGPNALDAYTE 476

Query: 484 VKQVT 488
            K ++
Sbjct: 477 QKYIS 481


Lambda     K      H
   0.318    0.135    0.422 

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: 688
Number of extensions: 31
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: 505
Length of database: 501
Length adjustment: 34
Effective length of query: 471
Effective length of database: 467
Effective search space:   219957
Effective search space used:   219957
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources