GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Dinoroseobacter shibae DFL-12

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-16246
         (477 letters)



>lcl|FitnessBrowser__Dino:3609503 Dshi_2887 succinic semialdehyde
           dehydrogenase (RefSeq)
          Length = 492

 Score =  308 bits (788), Expect = 4e-88
 Identities = 181/469 (38%), Positives = 257/469 (54%), Gaps = 5/469 (1%)

Query: 11  YIDGAFVE--SAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERA 68
           Y  GA+ +  S A   V NPA G +++ VP     E  RA+AAA AAQK WA + A +RA
Sbjct: 23  YFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRA 82

Query: 69  GHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIAS 128
             LRR    I  +A  +AR +T E GK  + A  EV + A ++++ AE A+RL GE I  
Sbjct: 83  QVLRRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIPG 142

Query: 129 DRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFA 188
             P   I + R+P+GVV  I PWNFP  +I RK APAL  G   + KP+E+TP +    A
Sbjct: 143 HLPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALA 202

Query: 189 RLVAETDLPRGVFNVV--CGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKL 246
            L     +P G+F V+    +  +G     +  V  ++FTGS + G  ++A AA  + K 
Sbjct: 203 VLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKC 262

Query: 247 NLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAA 306
           ++ELGG AP IV  DADL+ AV+     +  N+GQ C CA R+YVQ  V + F E++AAA
Sbjct: 263 SMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAAA 322

Query: 307 MAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPT 366
           +   + GD  AE  V +GPLIN   +EK+   +    A+G T+VTGG      G  + PT
Sbjct: 323 VEELKVGDGAAE-GVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTPT 381

Query: 367 VLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALR 426
           V+TG   + ++ REE FGPV P+    + DE IA+AND  +GL    + RD+ +      
Sbjct: 382 VVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSE 441

Query: 427 ELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYL 475
            L++G   IN            GV++SG+G    +HG+ EY     + L
Sbjct: 442 ALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICL 490


Lambda     K      H
   0.320    0.136    0.395 

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: 563
Number of extensions: 22
Number of successful extensions: 3
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: 477
Length of database: 492
Length adjustment: 34
Effective length of query: 443
Effective length of database: 458
Effective search space:   202894
Effective search space used:   202894
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, the preprint on GapMind for carbon sources, 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