GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Caulobacter crescentus NA1000

Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate CCNA_02321 CCNA_02321 O-succinylhomoserine sulfhydrylase

Query= BRENDA::Q1M0P5
         (380 letters)



>FitnessBrowser__Caulo:CCNA_02321
          Length = 394

 Score =  239 bits (609), Expect = 1e-67
 Identities = 138/383 (36%), Positives = 224/383 (58%), Gaps = 16/383 (4%)

Query: 5   TKLIHGGISEDATTGAVSVPIYQTSTYRQDAI--------GHHKGYEYSRSGNPTRFALE 56
           TKLI GGI+           +Y T  +  D+         G   G+ YSR  NPT    E
Sbjct: 12  TKLIRGGIARSQFMETAEA-LYLTQGFTYDSAEGADRRFAGEDPGFVYSRFNNPTVKMFE 70

Query: 57  ELIADLEGGVKGFAFASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLS 115
           + +A LEG     A A+G+A IHA +  L+++GDHV+ G  ++G    + ++ L + G+ 
Sbjct: 71  DRLALLEGAEVCRAQATGMASIHAALMGLVRAGDHVVAGRALFGSCRWIVSEWLPRFGVE 130

Query: 116 CTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFAT 175
            T +D +D    + A++PNTKA+ +ETPSNP+L+ITD+   + +A   G   IVDN FAT
Sbjct: 131 TTFVDATDPKAWEAAMRPNTKAVLVETPSNPVLEITDIRAVSELAHAVGAKVIVDNVFAT 190

Query: 176 PYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAI---GGVLGP 232
           P +Q PL LGAD+VV+S TK++ G   V+ G + T +EA+ +E  F+++++   G  L P
Sbjct: 191 PIFQKPLELGADVVVYSATKHIDGQGRVLGGAILT-SEAINEE--FYRDSLRHTGPSLSP 247

Query: 233 QDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRG 292
            ++W++ +G++TL LR++    +A  +A  + +H KV+ V YP  P HP + +AK QM G
Sbjct: 248 FNAWVMLKGLETLDLRVRRQADSAFALANTIAEHKKVQTVLYPFRPDHPGHNVAKAQMTG 307

Query: 293 FSGMLSFTLKNDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIR 352
              +++  L +   A  F+ +L++  +  +LG  +S+   P   TH  +P+ +R + G+ 
Sbjct: 308 GGTVIALDLGSREAAFKFLNALEIVDISNNLGDAKSMATHPPTTTHRSVPEAERPSLGVT 367

Query: 353 DGLVRLSVGIEHEQDLLEDLEQA 375
           +G VRLSVG+E  +DL  D+ +A
Sbjct: 368 EGGVRLSVGLESVEDLKRDVIRA 390


Lambda     K      H
   0.318    0.136    0.394 

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: 382
Number of extensions: 17
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: 380
Length of database: 394
Length adjustment: 30
Effective length of query: 350
Effective length of database: 364
Effective search space:   127400
Effective search space used:   127400
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: 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