GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Caulobacter crescentus NA1000

Align cystathionine beta-lyase (EC 4.4.1.8) (characterized)
to candidate CCNA_01491 CCNA_01491 cystathionine beta-lyase

Query= BRENDA::P06721
         (395 letters)



>FitnessBrowser__Caulo:CCNA_01491
          Length = 386

 Score =  304 bits (779), Expect = 2e-87
 Identities = 165/387 (42%), Positives = 237/387 (61%), Gaps = 14/387 (3%)

Query: 7   DTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFS 66
           +T+L++ G         VN  IQR S+++         A     + +L YG  G  T  +
Sbjct: 4   ETRLIHTGSEPARLGRTVNPPIQRGSTVLLPD------AASLYDDDQLTYGITGLSTPVA 57

Query: 67  LQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLG 126
           LQ A+ ELEG     L+P G AA+  ++LA ++ GD VL+ ++AY+P++ FC ++L + G
Sbjct: 58  LQNALAELEGATNVTLYPSGLAAITGAMLAVLKAGDEVLVVDSAYKPTRRFCDRVLGRFG 117

Query: 127 VTTSWFDPLIGADIVKHL-QPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMID 185
           VTT ++DP +  + +  L   +T+++ LE+PGS+T E+ D+PAI AA  +     + +ID
Sbjct: 118 VTTRYYDPKLSPEALMGLVTSSTRLIVLEAPGSLTFEMQDIPAIAAAANA--RGVLTLID 175

Query: 186 NTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGT-AVCNARCWEQLRENAYLMGQMV 244
           NTWAAG+LFK L  G+ +S+QA TKY+ GHSD  +G+ A C+    + L +  + +G  V
Sbjct: 176 NTWAAGLLFKPLAHGVTMSVQALTKYVGGHSDCFMGSVATCDDAVAKLLGDAMWDIGWSV 235

Query: 245 DADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDF 304
            +D AY   RGLRTL  RL +H E+ L +A WL E P+VARV HPALPG  GH  WKRDF
Sbjct: 236 SSDDAYTMLRGLRTLATRLPRHAENGLAIARWLQERPEVARVLHPALPGDAGHAIWKRDF 295

Query: 305 TGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEI 364
           TG+ GLF  VL K  + + +  +LD+  LF + +SWGGYESL L   P+  A   P   +
Sbjct: 296 TGACGLFGVVL-KPCSQKAVHAFLDSLKLFGLGFSWGGYESLALNCDPQLGARSIP---V 351

Query: 365 DFSGTLIRLHIGLEDVDDLIADLDAGF 391
           D  G L+R HIGLE ++DL ADL  GF
Sbjct: 352 DLEGPLLRFHIGLEGIEDLKADLRRGF 378


Lambda     K      H
   0.321    0.135    0.402 

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: 347
Number of extensions: 13
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: 395
Length of database: 386
Length adjustment: 31
Effective length of query: 364
Effective length of database: 355
Effective search space:   129220
Effective search space used:   129220
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