GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pedobacter sp. GW460-11-11-14-LB5

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

Query= SwissProt::P40732
         (405 letters)



>FitnessBrowser__Pedo557:CA265_RS15205
          Length = 378

 Score =  202 bits (513), Expect = 2e-56
 Identities = 125/383 (32%), Positives = 195/383 (50%), Gaps = 21/383 (5%)

Query: 29  VKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTS--NVFTNEPA 86
           V+ KG  ++D Q K++ID   GI V+ +GHCHPA+V+A++ Q ET  H      +   P 
Sbjct: 5   VRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMHLMVYGEYVQTPQ 64

Query: 87  LRLGRKLIDAT--FAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGR 144
           +   + L D          F+NSGTEA E A KLA+ Y        +   IA  NA+HG 
Sbjct: 65  VNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTG------RKGFIACKNAYHGS 118

Query: 145 SLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAA 204
           +    S+     YS G+GP    +  +  N+L  ++ + ++   AV +EPIQGE G++ +
Sbjct: 119 TQGAESLMESDFYSSGYGPFLPHVSFIEHNNLADLEKITNE-IAAVFIEPIQGEAGIRVS 177

Query: 205 TPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVS 264
              +++ LR  C E   LL+FDE+Q G GR+G +FA+ HY V PD+L  AK +GGG P+ 
Sbjct: 178 DLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGGMPIG 237

Query: 265 AMLTTQEIASAFH---VGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQH 321
           A +++ EI S      +  H +T+GG+P+ CA   A    +    ++  +  K Q F Q 
Sbjct: 238 AFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQLFKQL 297

Query: 322 LQAIDEQFDIFSDIRGMGLLIGAELKP-KYKGRARDFLYAGAEAGVMVLNAGADVMRFAP 380
           L     Q     +IRG GL++  E +  +   +  D            L+  ++ MR AP
Sbjct: 298 L-----QHPAIKEIRGKGLMLAVEFENFEINKKIIDACILDGVLSDWFLHC-SNSMRIAP 351

Query: 381 SLVVEEADIHEGMQRFAQAVGKV 403
            L++ + +I E      + V  V
Sbjct: 352 PLIITKEEIAEACTIILKNVNSV 374


Lambda     K      H
   0.322    0.137    0.412 

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: 392
Number of extensions: 24
Number of successful extensions: 5
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: 405
Length of database: 378
Length adjustment: 31
Effective length of query: 374
Effective length of database: 347
Effective search space:   129778
Effective search space used:   129778
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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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