GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2488 N515DRAFT_2488
           succinate-semialdehyde dehydrogenase /
           glutarate-semialdehyde dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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