GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Trichormus variabilis ATCC 29413

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::Q8BH00
         (487 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  294 bits (752), Expect = 5e-84
 Identities = 164/485 (33%), Positives = 269/485 (55%), Gaps = 9/485 (1%)

Query: 8   LMLENFIGGKFLPC--NSYIDSYDPST-GEVYCKVPNSGKEEIEAAVEAAREAFPAWSSR 64
           L  +N+I G++L     + ++S++P+   E+    P S  ++ + AV AAR+A+ +W   
Sbjct: 5   LNCQNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKV 64

Query: 65  SPQERSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHH 124
               R+  + R+ ++L Q  EELAQ  S++ GK +T AR  D+   V    + A      
Sbjct: 65  PAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGRRL 123

Query: 125 VSECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTS 184
             + T          TVR P+G+  LI+PWN P+ +  WK  PA+  GNTVI KP+E T 
Sbjct: 124 FGQTTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTP 183

Query: 185 VTAWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSA 244
             A    ++   AG+PPGVIN+V G G   G+ALV HP + L+SFTGS  T   + +   
Sbjct: 184 ACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCG 243

Query: 245 PHCKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFL 304
              K++ LE+GGKN  ++ EDA+LE  +   +  +F   G+ C  TSR+ + R I  +F 
Sbjct: 244 RTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFT 303

Query: 305 KRFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLP 364
               E T + ++G  ++P  ++G +I+   L++V  Y+  A+ EGA+IL G    ++   
Sbjct: 304 TMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIG---GEIVTE 360

Query: 365 LRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVW 424
            + + GYF  PT++ ++  + R   EEIFGPV  ++   + EE I   N  +YGL+++V+
Sbjct: 361 GQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVY 420

Query: 425 SKDVGRIHRVAKKLQSGLVWTNCWLI-RELNLPFGGMKSSGIG-REGAKDSYDFFTEIKT 482
           ++D+ R     + ++ G+ + N   I  E++LPFGG+K +G G RE    + D FTE K+
Sbjct: 421 TRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKS 480

Query: 483 ITIKY 487
           + + +
Sbjct: 481 VYVDF 485


Lambda     K      H
   0.319    0.134    0.404 

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: 532
Number of extensions: 27
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: 487
Length of database: 498
Length adjustment: 34
Effective length of query: 453
Effective length of database: 464
Effective search space:   210192
Effective search space used:   210192
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 Apr 09 2024. 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