GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Dyella japonica UNC79MFTsu3.2

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase

Query= SwissProt::Q9H2A2
         (487 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3729
          Length = 483

 Score =  473 bits (1217), Expect = e-138
 Identities = 237/483 (49%), Positives = 330/483 (68%), Gaps = 6/483 (1%)

Query: 8   LMLENFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRS 65
           L L N IDG+        +++ ++P+TGEV+   P S   +++AAV AA  A P W++  
Sbjct: 4   LRLANLIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATP 63

Query: 66  PQERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHT 125
            ++R+R+L ++ADL+E  L+EFA  ES+D GK L+LAR++DIPR+V N R+FA++ +  +
Sbjct: 64  SEQRARLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWS 123

Query: 126 SECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSV 185
           SE   M+ LG ++YT+R P+GV   ISPWNLPLYL TWKIAPA+AAGN V+AKPSE+T  
Sbjct: 124 SESHAME-LGAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPC 182

Query: 186 TAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP 245
           TA +L +L  +AG PPGV+NIV G GP VG+ALV H +V  +SFTGS  T  +I   +AP
Sbjct: 183 TAALLGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAP 242

Query: 246 HCKKLSLELGGKNPAIIFEDANL-DECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFL 304
             KKLSLELGGKNPAI+F DA+L D  +   VRS FANQGEICLC SR+ VQ+SIY  F 
Sbjct: 243 RFKKLSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFR 302

Query: 305 KRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLP 364
           +R++   R  +VG P +    +GAL+S+ H +KV   + +A AEG ++ CG   D L+LP
Sbjct: 303 ERYLAKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGG--DALALP 360

Query: 365 ARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVW 424
                G+++ PTVI  +  E+    +EIFGPV  ++PFD E + +  AN   YGLAA++W
Sbjct: 361 GPLAGGWYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLW 420

Query: 425 SSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTIT 484
           ++++ R HR   +L  G+VW NCWL+R+L  PFGG K SG+GREG  ++  FFTE K I 
Sbjct: 421 TTDLSRAHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNIC 480

Query: 485 VKH 487
           +++
Sbjct: 481 IRY 483


Lambda     K      H
   0.319    0.133    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: 625
Number of extensions: 25
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: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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