GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Pedobacter sp. GW460-11-11-14-LB5

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::Q8BH00
         (487 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  344 bits (883), Expect = 4e-99
 Identities = 187/485 (38%), Positives = 279/485 (57%), Gaps = 14/485 (2%)

Query: 11  ENFIGGKFLPC--NSYIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQE 68
           +N+IGGKF+     +Y D+  P  G+V+ K  +S KE++E AV+AA EAF  WS  S  E
Sbjct: 15  DNYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTE 74

Query: 69  RSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSEC 128
           RS++LN++A  +E +LE LA  E+ D GK +      D+P  V +FR+FA          
Sbjct: 75  RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134

Query: 129 TQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAW 188
           +++     +   V  P+G+   I PWN PL +  WK+APA+AAGN V+ KP+E T V+  
Sbjct: 135 SELDQ-NTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIM 193

Query: 189 MFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCK 248
           +  +L+    +PPGV+N+V G G  +G ALV++P+V   +FTGS PT   + Q +  +  
Sbjct: 194 VLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENII 252

Query: 249 KLSLELGGKNPAIIF------EDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSE 302
            ++LELGGK+P I F      +DA L++ +   V  +  NQGEIC C SR+ +Q  IY +
Sbjct: 253 PVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLIQEDIYEK 311

Query: 303 FLKRFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLS 362
           F+ + +E T+  K+G P D +  MGA  SK   EK+ +Y+   + EGA +L G  +++  
Sbjct: 312 FIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE-- 369

Query: 363 LPLRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAAT 422
           LP     GY++ PT+     ++ R   EEIFGPV  V  F + EE I  AN   YGL A 
Sbjct: 370 LPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAG 428

Query: 423 VWSKDVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKT 482
           VW++D   +++V + +Q+G VW N +       PFGG K SG+GRE  K     + + K 
Sbjct: 429 VWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKN 488

Query: 483 ITIKY 487
           + I Y
Sbjct: 489 MLISY 493


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: 531
Number of extensions: 20
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: 501
Length adjustment: 34
Effective length of query: 453
Effective length of database: 467
Effective search space:   211551
Effective search space used:   211551
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.

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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