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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources