GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Shewanella oneidensis MR-1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)

Query= BRENDA::Q8BH00
         (487 letters)



>FitnessBrowser__MR1:202599
          Length = 498

 Score =  297 bits (760), Expect = 6e-85
 Identities = 171/481 (35%), Positives = 264/481 (54%), Gaps = 16/481 (3%)

Query: 13  FIGGKFLPCNS--YIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPA--WSSRSPQE 68
           FI G++   +S    D   P  G +   V +    +   AV  ARE F +  WS  +P +
Sbjct: 24  FINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAPVK 83

Query: 69  RSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFF--ASSNLHHVS 126
           R  V+ R A++LE++  ELA  E+ D GK +  ++ +D+  +    R+   A   L+   
Sbjct: 84  RKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYDEL 143

Query: 127 ECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVT 186
             T  + +G +    R PVG+   I PWN PL +  WK+ PA+  GN+VI KPSE + +T
Sbjct: 144 APTAHNEIGMI---TREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLT 200

Query: 187 AWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP- 245
           A    +L  +AG+P GV+N++ G G  VG+AL  H +V  + FTGS   A+++   +   
Sbjct: 201 AIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260

Query: 246 HCKKLSLELGGKNPAIIFEDA-NLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFL 304
           + K++ LE GGK+P I+F DA +L+    A   +   NQGE+C   SR+ V+  +  E +
Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELV 320

Query: 305 KRFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLP 364
               E    W+ G P +P+   GA++ K  L+ + SY+   Q EGA ++ G         
Sbjct: 321 GLIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGG-----QQV 375

Query: 365 LRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVW 424
           L    G ++ PTV +++K++ +  +EEIFGPV  V+ F+  EE I  AN   YGLAA VW
Sbjct: 376 LAETGGVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVW 435

Query: 425 SKDVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTIT 484
           + D+ + H+ AK L+SG+VW N +   ++  PFGG K SG GR+ +  S+D +TEIK   
Sbjct: 436 TADISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHSFDKYTEIKATW 495

Query: 485 I 485
           I
Sbjct: 496 I 496


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: 545
Number of extensions: 24
Number of successful extensions: 5
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 Sep 17 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