GapMind for catabolism of small carbon sources

 

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

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase

Query= reanno::WCS417:GFF2142
         (499 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2488
          Length = 463

 Score =  197 bits (501), Expect = 7e-55
 Identities = 140/443 (31%), Positives = 211/443 (47%), Gaps = 19/443 (4%)

Query: 25  NPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRARVLFEYLHLLRERKDDLA 84
           NP TGE       A+   V++A+  AQA F  W D     R +VL +   LLRE     A
Sbjct: 7   NPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQYA 66

Query: 85  RIIVAEHGKVFTDAQGEVDRGIDILEFACG------IPNLLKGEHSDQVSRGMDNWTMRQ 138
           +++  E GKV  +A+GEV+    ILE+          P  L   H         +W    
Sbjct: 67  KVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQ----SWVEHV 122

Query: 139 PLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASLFMAELLREAGLPKGV 198
           P G++  V P+NFP    + +    +AAGN  ILK +   P  +     L REAGLP+G 
Sbjct: 123 PQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGG 182

Query: 199 FNVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYI-YETGARNGKRVQGLGGAKNHMVVM 257
           F  +   ++ + A+IE P V+ V+  GS      +  + G    K    LGGA +  VV+
Sbjct: 183 FTNLYATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGA-DAFVVL 241

Query: 258 PDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALTERAKHLRITDGRDLK 317
            DAD++K V   +   + +AG+ C +    ++V ++ D  +         LR  D  +  
Sbjct: 242 ADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEPS 301

Query: 318 AEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPGLENGFWLGATLFDHVTEE 377
             + P+ SR A++ +   +EQ V  GA++ + G + VP+      G +    L  HV+++
Sbjct: 302 TTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAE-VPS-----RGAFFRPVLLSHVSDD 355

Query: 378 MSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDGNIAREFARRIEVGMVG 437
                 E FGPV   +R  D A+AI++ N   FG G S FT D     E A++I  GMV 
Sbjct: 356 NPARYWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVY 415

Query: 438 INVPISVPMAWHGFGGWKKSLFG 460
           IN P  V  A   FGG ++S +G
Sbjct: 416 INHPTGV-AADLPFGGVRRSGYG 437


Lambda     K      H
   0.320    0.136    0.407 

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: 511
Number of extensions: 24
Number of successful extensions: 4
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: 499
Length of database: 463
Length adjustment: 34
Effective length of query: 465
Effective length of database: 429
Effective search space:   199485
Effective search space used:   199485
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