GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Verminephrobacter eiseniae EF01-2

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein

Query= SwissProt::Q9H2A2
         (487 letters)



>NCBI__GCF_000015565.1:WP_011810430.1
          Length = 798

 Score =  311 bits (798), Expect = 4e-89
 Identities = 177/463 (38%), Positives = 262/463 (56%), Gaps = 21/463 (4%)

Query: 12  NFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQER 69
           +FI G+F+  +   Y + ++P+T E   RV +    +I+ AV AAR+A P+WS  S  +R
Sbjct: 36  HFIHGEFVAPAQNEYFEVFNPATEERLARVAHGSDADIDQAVAAARQALPAWSGLSGHQR 95

Query: 70  SRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECT 129
           +R L  +A  L++    FA  E+ D GKT+  +R +DIP  V++F        HH     
Sbjct: 96  ARYLYAIARHLQKHARFFAVLETMDNGKTIRESRDIDIPLVVRHF-------YHHAGWAQ 148

Query: 130 QMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWM 189
            +D      +     VGV G I PWN PL +L WK+APA+AAGNTV+ KP+E T +TA  
Sbjct: 149 LLDS----EFPAHQAVGVCGQIVPWNFPLLMLAWKVAPALAAGNTVVLKPAEFTPLTALA 204

Query: 190 LCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKK 249
             +L  + G+P GV+NIV G G   G +LV+H  V  I+FTGS      I + +A   KK
Sbjct: 205 FAELCVEVGLPAGVLNIVTGDG-HTGASLVNHAGVDKIAFTGSTAVGRLIRRATAGTDKK 263

Query: 250 LSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVE 309
           LSLELGGK+P I+F+DA+LD  +   V S + NQG++C   SRI VQ+S+ + F  +   
Sbjct: 264 LSLELGGKSPFIVFDDADLDAAVEGVVDSIWFNQGQVCCAGSRILVQESVAARFGDKLRA 323

Query: 310 ATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQA 369
             RK ++G P D    +GA++ +  L+++R  V+   A+G   W       L  P+   +
Sbjct: 324 RMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRADGLSCW----QTALDAPS---S 376

Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429
           G+F  PT   D+        EEIFGPV   + F + +E +  AN+ +YGLAA++WS N+ 
Sbjct: 377 GHFFAPTFFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANHSRYGLAASLWSENID 436

Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKD 472
               VA +L +G+VW N   + +    FGG + SG GREG ++
Sbjct: 437 VCLTVAAQLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGRE 479



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 68/245 (27%), Positives = 105/245 (42%), Gaps = 20/245 (8%)

Query: 13  FIDGKFL-PCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71
           +I GK + P S Y       +G +        + +I  AV+ AR+A  +WS  S   R++
Sbjct: 527 YIGGKQVRPDSGYSFGVRSGSGALLGHAGFGNRKDIRNAVETARKA-GNWSQASGHARAQ 585

Query: 72  VLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQM 131
           VL   A+ L    + F        G + A A         Q F    +   H+ +   + 
Sbjct: 586 VLYYFAENLGARAQTFIAHLQAIDGISEAAAS--------QQFEQVLARVFHYAAMADKH 637

Query: 132 DHLGCMHYTVRA--------PVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELT 183
           D  G +H T+ A        P GV G+ SP + PL        P +A GN V+  P    
Sbjct: 638 D--GSVHSTLTAHVTLAMNEPFGVVGVRSPAHTPLLAALSLALPLLATGNRVVLVPPPDA 695

Query: 184 SVTAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLS 243
           S+    L ++LD + +P GV+NIV+G    + E L  H +V  + + G    A R+   S
Sbjct: 696 SLMFADLYQVLDTSDMPAGVLNIVWGDSDELAEVLALHDDVDALWYFGPAAGAARVQAAS 755

Query: 244 APHCK 248
           A + K
Sbjct: 756 AGNLK 760


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: 914
Number of extensions: 24
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 487
Length of database: 798
Length adjustment: 37
Effective length of query: 450
Effective length of database: 761
Effective search space:   342450
Effective search space used:   342450
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: 54 (25.4 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