GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Flavobacterium glycines Gm-149

Align (R)-citramalate synthase (EC 2.3.1.182) (characterized)
to candidate WP_066328410.1 BLR17_RS00960 2-isopropylmalate synthase

Query= reanno::Btheta:351386
         (499 letters)



>NCBI__GCF_900100165.1:WP_066328410.1
          Length = 507

 Score =  601 bits (1550), Expect = e-176
 Identities = 297/498 (59%), Positives = 383/498 (76%), Gaps = 2/498 (0%)

Query: 1   MDTTLRDGEQTSGVSFVPHEKLMIARLLLEDLKVDRVEVASARVSEGEFEAVKMICDWAA 60
           MDTTLRDGEQTSGVSF   EKL IA+LLLE+L+VDR+E+ASARVSEGEFE VK I  WA 
Sbjct: 9   MDTTLRDGEQTSGVSFSAAEKLTIAQLLLEELQVDRIEIASARVSEGEFEGVKGIMTWAE 68

Query: 61  RRNLLQKVEVLGFVDGHTSVDWIQRTGCRVINLLCKGSLKHCTQQLKKTPEEHIADIINV 120
            +    K+EVL FVD   S++W++++G +V NLL KGSL H T QLKKTPE+H ++I   
Sbjct: 69  TKGYTDKIEVLTFVDKGLSIEWMKKSGAKVQNLLTKGSLNHLTHQLKKTPEQHFSEIAES 128

Query: 121 VHYADEQDIGVNVYLEDWSNGMKDSPEYVFQLMDGLKQTSIRRYMLPDTLGILNPLQVIE 180
           +  A E  I  NVYLEDWSNGM++S EYV+Q +D +    ++R +LPDTLG+L P +  E
Sbjct: 129 IALATENGIATNVYLEDWSNGMRNSSEYVYQYLDFISTQPVKRILLPDTLGVLIPSETFE 188

Query: 181 YMRKMKKRYPNTHFDFHAHNDYDLAVSNVLAAVLSGVRGLHTTINGLGERAGNAPLSSVQ 240
           Y+ ++ KRYPN HFDFHAHNDYDL+V+NV+ A+ +GV GLH T+NG+GERAGNAPL+S  
Sbjct: 189 YISEITKRYPNIHFDFHAHNDYDLSVANVMEALKAGVHGLHVTVNGMGERAGNAPLASTI 248

Query: 241 AILKDHFNAM-TNIDESRLNDVSRVVESYSGIVIPANKPIVGENVFTQVAGVHADGDNKN 299
           A++ D    +   + E+ L  VS++VE+++G  IPANKPIVG+NVFTQ AG+HADGDNKN
Sbjct: 249 AVINDFMPEIEIGVKETSLYSVSKLVETFTGYRIPANKPIVGDNVFTQTAGIHADGDNKN 308

Query: 300 NLYCNDLLPERFGRKREYALGKTSGKANIRKNLEDLGLELDEDAMRKVTERIIELGDKKE 359
           NLY NDLLPERFGRKR+YALGKTSGKANI KNL++LGL+L+++ ++ VT+RIIELGDKKE
Sbjct: 309 NLYFNDLLPERFGRKRKYALGKTSGKANIEKNLQELGLQLNQEDLKLVTQRIIELGDKKE 368

Query: 360 LVTQEDLPYIVSDVLKHGAIGEKVKLKSYFVNLAHGLKPMATLKIEINGKEYEESSSGDG 419
            VT+EDLPYI+SDVL      EK+ ++SY ++ A G++P  TL ++I+G+  EE + GDG
Sbjct: 369 TVTKEDLPYIISDVLDSHTYQEKITVESYLLSHAKGMRPSTTLCLKIDGQIIEEHAQGDG 428

Query: 420 QYDAFVRALRKIYKVTLGRKFPMLTNYAVSIPPGGRTDAFVQTVITWNYDEQVFRTRGLD 479
           Q+DAF+ AL KIYK T     P L +YAV IPPG  +DA  +T+ITW  D + F+TRGLD
Sbjct: 429 QFDAFMNALAKIYK-TKKMTLPKLIDYAVRIPPGSSSDALCETIITWVNDGKEFKTRGLD 487

Query: 480 ADQTEAAIKATMKMLNLL 497
           +DQT AAI AT KMLN++
Sbjct: 488 SDQTVAAIIATQKMLNVV 505


Lambda     K      H
   0.318    0.135    0.390 

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: 727
Number of extensions: 21
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: 499
Length of database: 507
Length adjustment: 34
Effective length of query: 465
Effective length of database: 473
Effective search space:   219945
Effective search space used:   219945
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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