GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Nocardioides daejeonensis MJ31

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_110207793.1 DNK54_RS15005 aldehyde dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>NCBI__GCF_003194585.1:WP_110207793.1
          Length = 501

 Score =  252 bits (643), Expect = 3e-71
 Identities = 165/488 (33%), Positives = 248/488 (50%), Gaps = 22/488 (4%)

Query: 37  HYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKT--WKDWP 94
           HY  +I G W D  + +   +P A  E+V T AK G AE +AA+ AA  A     W++ P
Sbjct: 5   HYQNFINGAWTDNGQVLEVRSP-ATGELVATVAKGGAAEIDAAVAAAKAAHAAGVWRNTP 63

Query: 95  QEDRSRLLLKAAALMRRRKRELEATLVYEVGKNW-VEASADVAEAIDFIEYYARAALRYR 153
             +R+ L+   A  +  R  EL A    E G    V  +  V  +I  +++ A  A  Y 
Sbjct: 64  PAERAALINAVAGDLAGRLEELAALQSRENGATIRVTGALHVGLSIANMQFIAAQAAEYE 123

Query: 154 YPAV--EVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAED 211
           +     E+ P P E       PLG    I PWN P+      +   +A GNTV+ KP E 
Sbjct: 124 FEKAGPEIGPVPAEGILR-REPLGVVGAIVPWNIPLLTIVWKVTPALAAGNTVVLKPDEH 182

Query: 212 AVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEA 271
           A ++  ++ + F  AG P GV+N + G G + GA L +HP  R I FTGS EVG  I   
Sbjct: 183 APLLALELAKAFEAAGLPAGVLNVVVGEGHDAGARLSQHPDVRKIGFTGSTEVGKSI--- 239

Query: 272 AGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILT 331
              L       KR  +E GGK   I+ + AD D+A +G + +     G+ C A +RL++ 
Sbjct: 240 ---LGASADNMKRVTLELGGKGPNILLDDADLDVAIDGAIYACMANNGEACEAGTRLLVP 296

Query: 332 QGAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGG 389
               + ++ER++ R   + +G P +   D+GP+++A+Q  +VL++I   + +G ++ +GG
Sbjct: 297 NSRKDEIVERLVARVGTMKIGNPLDPATDIGPLITADQRDRVLAHIAKAETQGAKVAIGG 356

Query: 390 KRLEGE----GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGL 445
               GE    GYF+ PTV T+V P   +A EE+FGPVLSV+      EA+ +ANDT YGL
Sbjct: 357 SAPAGEEFANGYFVEPTVLTDVTPSMTVACEEVFGPVLSVLGYDTVDEAIAIANDTEYGL 416

Query: 446 TGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRL 505
           + GV+      +    R+   G +Y N      L    PFGG+K SG   + G  + L  
Sbjct: 417 SAGVWGTDETRVLDVARQLEAGMIYVND--WHVLHPAYPFGGYKQSGL-GREGGPNALDA 473

Query: 506 FLEMKAVA 513
           + E K ++
Sbjct: 474 YTEQKYIS 481


Lambda     K      H
   0.319    0.137    0.403 

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: 643
Number of extensions: 31
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: 516
Length of database: 501
Length adjustment: 34
Effective length of query: 482
Effective length of database: 467
Effective search space:   225094
Effective search space used:   225094
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 (21.7 bits)
S2: 52 (24.6 bits)

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

Links

Downloads

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:

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