Aligments for a candidate for dapC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapC in Shewanella loihica PV-4

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)

Query= curated2:Q7N9E5
         (403 letters)



>lcl|FitnessBrowser__PV4:5210744 Shew_3172 4-aminobutyrate
           aminotransferase (RefSeq)
          Length = 426

 Score =  238 bits (607), Expect = 2e-67
 Identities = 147/405 (36%), Positives = 223/405 (55%), Gaps = 37/405 (9%)

Query: 29  RGQGSRVWDQHGKEYIDFAGGIAVVALGHCHPTLVDVLKQQGEKLWHISNIFTN--EPAL 86
           R   + +WD  GK YIDF  GIAV   GH HP +V  +K Q +   H   +  N  E A+
Sbjct: 28  RALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTC-VMVNPYESAV 86

Query: 87  ILAQKL---IDATFAERVFFANSGAEANEAAFKLARHYAIARHNPYKTKIIAFHQGFHGR 143
            LA++L         ++  F  +GAEA E   K+AR +   R       +IAF+ GFHGR
Sbjct: 87  ALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRG------VIAFNGGFHGR 140

Query: 144 TLFTVSVGGQ-PKYADGFGPKPADIIHVPF-------NDLDAVKAV-----IDDHTC--- 187
           T  T+++ G+   Y   FGP   DI H P+       +  D++KA+     +D   C   
Sbjct: 141 TNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKDSLKAIEHLFKVDIAPCDVA 200

Query: 188 AVVLEPVQGEGGVTAAAPAFIHGVRELCDKHQVLLVFDEVQSGMGRTGKLFSYMHYDVTP 247
           A+V+EPVQGEGG  AA P F+  +R LCD+H ++LV DE+Q+G GRTGK+FS  H  V P
Sbjct: 201 AIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQTGFGRTGKMFSCEHAGVEP 260

Query: 248 DIITTAKALGNGFPISAMLTTVNIASVMTPGAHGTTYGGNPLACAVANVAFDIINTPAVL 307
           D++T AK +  GFP++A++    I     PG  G TYGG+P+ C  A    +++    ++
Sbjct: 261 DLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVLEVMQEEQLV 320

Query: 308 AGVEKRHNLMVNFLNDINQKY-SIFGEIRGKGLLIGAEL------KAPHQGKAKDILQLA 360
               K  +     L+ + ++Y  + GE+R +G +I  EL      + P+    + I+  A
Sbjct: 321 ERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVIDGDIEQPNTALTQAIIANA 380

Query: 361 AENGLMLLSAG--GDVLRFTPSLIISEEEIAQGMERLEQVINQLV 403
           A +GL+LL+ G  G+V+RF P+L IS+E +A+G+ + + +   LV
Sbjct: 381 AAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLFESLV 425


Lambda     K      H
   0.321    0.138    0.410 

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: 468
Number of extensions: 20
Number of successful extensions: 6
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: 403
Length of database: 426
Length adjustment: 31
Effective length of query: 372
Effective length of database: 395
Effective search space:   146940
Effective search space used:   146940
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or see changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis