GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609503
          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 (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