GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Algiphilus aromaticivorans DG1253

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_043765072.1 U743_RS01785 aldehyde dehydrogenase family protein

Query= BRENDA::Q72IB9
         (516 letters)



>NCBI__GCF_000733765.1:WP_043765072.1
          Length = 506

 Score =  217 bits (552), Expect = 9e-61
 Identities = 168/480 (35%), Positives = 241/480 (50%), Gaps = 40/480 (8%)

Query: 34  FGRHYPLYIGGEWV--DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWK 91
           F   Y  +IGG+WV  ++ +   +++P    ++    A++  A+ E AL+AA  A   W 
Sbjct: 15  FKSRYDNFIGGDWVAPESGKYFDNVSPVTGGKIC-EIARSEAADVEKALDAAHAARARWA 73

Query: 92  DWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEAS-ADVAEAIDFIEYYARAAL 150
           +    +RS +L   A  M      L     ++ GK   E++ ADV  AID   Y+A  A+
Sbjct: 74  NTSTTERSNILNAIAQRMEDNLEALAQAETWDNGKAVRESTVADVPLAIDHFRYFA-GAI 132

Query: 151 RYRYPAVEVVPYPGEDNES----FYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIA 206
           R +  ++ ++     D ++    F+ PLG    I PWNFP+ +    +   +A GN V+ 
Sbjct: 133 RAQEGSISMI-----DEQTVAYHFHEPLGVVGQIIPWNFPLLMAVWKLAPALAAGNCVVI 187

Query: 207 KPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGL 266
           KPAE          E+  +   PPGV+N + G G E G  L   PR     FTG    G 
Sbjct: 188 KPAEQTPASILHWMEMIADL-LPPGVINIVNGFGLEAGKPLASSPRIAKAAFTGETTTGR 246

Query: 267 KIYE-AAGRLAPGQTWFKRAYVETGGK------DAIIVDETADFDLAAEGVVVSAYGFQG 319
            I + AA  L P         +E GGK      + ++ ++ A FD A EG V+ A   QG
Sbjct: 247 MIMQYAAQNLIP-------VTLELGGKSPNVFFEDVMREDDAYFDKAIEGFVLFALN-QG 298

Query: 320 QKCSAASRLILTQGAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEI 378
           + C+  SR ++ +  ++  +ER LKR E + +G P   +  +G   S+EQ  K+LSY +I
Sbjct: 299 EVCTCPSRALIQESIFDRFMERALKRVEAIQMGDPLSMDTMMGAQASSEQMEKILSYFDI 358

Query: 379 GKNEGQLVLGG---KRLEGE---GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFA 432
           GK EG  VL G    +L+GE   GY+I PTVF     K R+ QEEIFGPV+SV   KD A
Sbjct: 359 GKQEGAEVLTGGGRAQLDGELANGYYIKPTVFRG-HNKMRVFQEEIFGPVVSVTTFKDEA 417

Query: 433 EALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSG 492
           EALE+ANDT YGL  GV+SR         R    G ++ N     A      FGG+K SG
Sbjct: 418 EALEIANDTLYGLGAGVWSRDANICYRMGRGIQAGRVWTN--CYHAYPAHAAFGGYKQSG 475


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: 584
Number of extensions: 38
Number of successful extensions: 8
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: 506
Length adjustment: 35
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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.

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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