GapMind for catabolism of small carbon sources

 

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

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-16244
         (495 letters)



>NCBI__GCF_000015565.1:WP_011810430.1
          Length = 798

 Score =  352 bits (903), Expect = e-101
 Identities = 189/461 (40%), Positives = 273/461 (59%), Gaps = 14/461 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI+ EFV     + F   +P+TEE + +V      DID AV AA  A   +WS      R
Sbjct: 37  FIHGEFVAPAQNEYFEVFNPATEERLARVAHGSDADIDQAVAAARQAL-PAWSGLSGHQR 95

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142
            + LY +A  + +HA   A +E +DNGK++  S+  D+ L   +F   AGW   +     
Sbjct: 96  ARYLYAIARHLQKHARFFAVLETMDNGKTIRESRDIDIPLVVRHFYHHAGWAQLLDSE-- 153

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
                   +   + +GVCGQI+PWNFPLLM +WK+ P L  G T VLK AE TPL+AL  
Sbjct: 154 --------FPAHQAVGVCGQIVPWNFPLLMLAWKVAPALAAGNTVVLKPAEFTPLTALAF 205

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
           A L  E G P GV+N+V+G G T GA + +H  + K+AFTGSTA GR I +A A ++ KK
Sbjct: 206 AELCVEVGLPAGVLNIVTGDGHT-GASLVNHAGVDKIAFTGSTAVGRLIRRATAGTD-KK 263

Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322
           ++LELGGKSP IVFDDAD+ + ++ +V  I++N G+VCCAGSRI VQE +  +   + + 
Sbjct: 264 LSLELGGKSPFIVFDDADLDAAVEGVVDSIWFNQGQVCCAGSRILVQESVAARFGDKLRA 323

Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPT 382
               L+IG+P  +   +GA   ++QL +I + ++ G+ +G +         + G+F  PT
Sbjct: 324 RMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRADGLSCWQTALDAPSSGHFFAPT 383

Query: 383 IFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSN 442
            F DV   H + ++EIFGPVV    F+T++E +ALAN S YGLAA + + N+   ++V+ 
Sbjct: 384 FFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANHSRYGLAASLWSENIDVCLTVAA 443

Query: 443 KINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNY 483
           ++ +G +WVN  N F     FGGY +SG GRE G E +  Y
Sbjct: 444 QLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGREGMHEY 484



 Score = 78.6 bits (192), Expect = 8e-19
 Identities = 64/210 (30%), Positives = 94/210 (44%), Gaps = 5/210 (2%)

Query: 58  EDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADT-LAHIEALDNGKSLMCS 116
           +DI +AVE A  A   +WS +    R +VLY  A+ +   A T +AH++A+D       S
Sbjct: 560 KDIRNAVETARKA--GNWSQASGHARAQVLYYFAENLGARAQTFIAHLQAIDGISEAAAS 617

Query: 117 KGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWK 176
           +    + A  F   A   DK  GSV  T   H      EP GV G   P + PLL A   
Sbjct: 618 QQFEQVLARVFHYAA-MADKHDGSVHSTLTAHVTLAMNEPFGVVGVRSPAHTPLLAALSL 676

Query: 177 LGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKI 236
             P+L TG   VL       L    L  ++  +  P GV+N+V G        ++ H  +
Sbjct: 677 ALPLLATGNRVVLVPPPDASLMFADLYQVLDTSDMPAGVLNIVWGDSDELAEVLALHDDV 736

Query: 237 KKVAFTGSTATGRHIMKAAAESNLKKVTLE 266
             + + G  A G   ++AA+  NLK   ++
Sbjct: 737 DALWYFG-PAAGAARVQAASAGNLKSTWVQ 765


Lambda     K      H
   0.316    0.133    0.389 

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: 867
Number of extensions: 38
Number of successful extensions: 8
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: 495
Length of database: 798
Length adjustment: 38
Effective length of query: 457
Effective length of database: 760
Effective search space:   347320
Effective search space used:   347320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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