GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Dyella japonica UNC79MFTsu3.2

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase

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



>FitnessBrowser__Dyella79:N515DRAFT_2488
          Length = 463

 Score =  224 bits (570), Expect = 6e-63
 Identities = 145/449 (32%), Positives = 224/449 (49%), Gaps = 3/449 (0%)

Query: 27  NPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKIRADAGRIA 86
           NP  G  +   P+A+  EV +AL  A+A  + W       R   L++ A  +R    + A
Sbjct: 7   NPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQYA 66

Query: 87  RTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEG-EIIASDRPG-ENIFLFRKPLGV 144
           + +TLE GK+   AE EV   A  L+Y A+ A +L   E ++S  P     ++   P G+
Sbjct: 67  KVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHVPQGI 126

Query: 145 VAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVFNVV 204
           +  + PWNFP++ I R  AP L  GN +++K +   P     F RL  E  LP+G F  +
Sbjct: 127 LLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGGFTNL 186

Query: 205 CGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADADL 264
                   A+   P V  ++ TGS   GA + A A   L K  +ELGG    +VLADADL
Sbjct: 187 YATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVVLADADL 246

Query: 265 ELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAEPEVEMG 324
           + AV+     R  N+GQVC  ++R+ V  ++ + F+E+  A +A  R GDP+ EP   + 
Sbjct: 247 DKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPM-EPSTTLA 305

Query: 325 PLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREEIFG 384
           P+ +R  ++ +  ++  A+A GA +   GA     G  ++P +L+    D      E FG
Sbjct: 306 PMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARYWEFFG 365

Query: 385 PVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFEAMQ 444
           PV  +    D  +AI +AND  +GL  SVFT D+   +   +++  G  YIN     A  
Sbjct: 366 PVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPTGVAAD 425

Query: 445 GFHAGVRKSGIGGADGKHGLYEYTHTHVV 473
               GVR+SG G      G+ E+ +  ++
Sbjct: 426 LPFGGVRRSGYGRELTGLGIKEFVNHKLI 454


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: 492
Number of extensions: 24
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: 463
Length adjustment: 33
Effective length of query: 444
Effective length of database: 430
Effective search space:   190920
Effective search space used:   190920
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: 51 (24.3 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