GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3729 N515DRAFT_3729
           aminomuconate-semialdehyde/2-hydroxymuconate-6-
           semialdehyde dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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