GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Azospirillum thiophilum BV-S

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_045582953.1 AL072_RS17755 aldehyde dehydrogenase

Query= BRENDA::Q8BH00
         (487 letters)



>NCBI__GCF_001305595.1:WP_045582953.1
          Length = 503

 Score =  325 bits (833), Expect = 2e-93
 Identities = 181/480 (37%), Positives = 268/480 (55%), Gaps = 12/480 (2%)

Query: 14  IGGKFLPCNS--YIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAF--PAWSSRSPQER 69
           IGG+F+   S  YI SYDP+T E + ++ ++G E+++ AV AAR AF  PAW   +  +R
Sbjct: 17  IGGRFVEPKSGRYIPSYDPTTAEPWYELADAGPEDVDDAVAAARAAFVDPAWRRMTQSDR 76

Query: 70  SLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTM--DIPRSVLNFRFFASSNLHHVSE 127
             ++ RLA+++  + EELA  E++D GK +   R     +P S   + +FA        +
Sbjct: 77  GKLVRRLAELILVNAEELALMETRDNGKLIKEMRAQMRAMPDS---YTYFAGMADKLQGD 133

Query: 128 CTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTA 187
              ++ L  +++ +R P+G+ G+I+PWN PL LLT  +AP +A GNTV+ KPSE  + + 
Sbjct: 134 TIPVNKLDMLNFNLREPLGVVGMITPWNSPLMLLTGTLAPCLAIGNTVVIKPSEHATAST 193

Query: 188 WMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHC 247
               +L+ +AG P GV+N+V G G   GEAL  HP +  I FTGS  T  RI   +A + 
Sbjct: 194 LALAELVAEAGFPAGVVNVVSGAGATAGEALTRHPGIAKIVFTGSTQTGSRIAANAAGNL 253

Query: 248 KKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRF 307
               +ELGGK+P ++F D ++E  +   V   FA  G+ C+  SR FV+ SIY  F++  
Sbjct: 254 VPCQMELGGKSPHVVFGDVDIERAVNGVVAGVFAAAGQTCVAGSRCFVEASIYDRFVEAL 313

Query: 308 VEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRN 367
           V  T +  VG P +   ++G L     L KV  YV   Q +GAR+  G    Q +     
Sbjct: 314 VARTGRIAVGHPMEEGTDIGPLALSPQLAKVEEYVASGQRDGARLAAGGRRPQAA---GL 370

Query: 368 QAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKD 427
             G++  PTV+ D +++   M +EIFGPV  VVPF SE+E+I  AN  RYGLA+ +W+ D
Sbjct: 371 DRGWYFEPTVLADARNDMGFMRDEIFGPVVGVVPFASEDEMIAMANDTRYGLASGIWTGD 430

Query: 428 VGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITIKY 487
           + R  R A ++ +G VW N +         GG K SG GR G  D    F+  K + I Y
Sbjct: 431 IDRAMRFATRIDAGTVWINTYRAAAYMSSNGGFKQSGYGRRGGFDVMREFSRSKNVVIDY 490


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: 538
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: 487
Length of database: 503
Length adjustment: 34
Effective length of query: 453
Effective length of database: 469
Effective search space:   212457
Effective search space used:   212457
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