GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Streptomyces kebangsaanensis SUK12

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::Q8BH00
         (487 letters)



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  355 bits (910), Expect = e-102
 Identities = 182/455 (40%), Positives = 272/455 (59%), Gaps = 5/455 (1%)

Query: 29  DPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSLVLNRLADVLEQSLEELA 88
           DP+TGE       +G ++++AAV AAREAFP W+  +P +RS  L+R A+VL    E+ A
Sbjct: 42  DPATGEEVHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDFA 101

Query: 89  QAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQMSHLGCMHYTVRTPVGIA 148
           +AES   GK L L R  D+P ++ N  FFA +  H   +           Y  R P+G+ 
Sbjct: 102 RAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRREPIGVV 161

Query: 149 GLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPGVINIVF 208
           G I+PWN PL +  WK+ PAIAAGNT++ KP+E+T +T+ +F +   +AG+P GVINIV 
Sbjct: 162 GSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINIVT 221

Query: 209 GTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFEDANL 268
           GTG   GE LV HP+V ++SFTGS    +R+ +++    K+L LELGGK P ++F+DA+L
Sbjct: 222 GTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLELGGKAPFVVFDDADL 281

Query: 269 EECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDPSANMGA 328
           E  +   V  +  N G+ C   +R +VQR +Y EF+ R        ++G P  P  ++G 
Sbjct: 282 EAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLGDPFAPGTDLGP 341

Query: 329 LISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPTVITDIKDESRCM 388
           LIS  H ++V  +V +A+   AR++ G    Q  L    + G +  PT+I     +S  +
Sbjct: 342 LISHVHRDRVAGFVDRARAY-ARVVTGGEAPQGEL----KNGAYYRPTLIAGAAQDSEIV 396

Query: 389 TEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGLVWTNCW 448
             EIFGPV  V+PFDS++E I  AN   YGLAA+ WS+DV R +R  +++++G VW N  
Sbjct: 397 QSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGCVWVNDH 456

Query: 449 LIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTI 483
           +     +P GG K SG G++ +  S++ +T+IK +
Sbjct: 457 IPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHV 491


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: 535
Number of extensions: 24
Number of successful extensions: 3
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: 511
Length adjustment: 34
Effective length of query: 453
Effective length of database: 477
Effective search space:   216081
Effective search space used:   216081
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