Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate BWI76_RS21465 BWI76_RS21465 bifunctional chorismate mutase/prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__Koxy:BWI76_RS21465 Length = 386 Score = 679 bits (1751), Expect = 0.0 Identities = 342/385 (88%), Positives = 360/385 (93%) Query: 1 MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60 MT ENPLLALR+KISALDEKLLALLAERR LAVEVGKAKL SHRPVRDIDRERDLLERL+ Sbjct: 1 MTEENPLLALRDKISALDEKLLALLAERRGLAVEVGKAKLASHRPVRDIDRERDLLERLM 60 Query: 61 TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSARIAFLGPKGSYSHLAA 120 TLGK HHLDAHYITRLFQLIIEDSVLTQQ LLQQHLNKINPHSAR+AFLGPKGSYSHLAA Sbjct: 61 TLGKKHHLDAHYITRLFQLIIEDSVLTQQTLLQQHLNKINPHSARVAFLGPKGSYSHLAA 120 Query: 121 RQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLSI 180 RQYAARHFEQFIESGCAKFADIF QVETGQADYAVVPIENTSSG INDVYDLLQHT+LSI Sbjct: 121 RQYAARHFEQFIESGCAKFADIFEQVETGQADYAVVPIENTSSGGINDVYDLLQHTTLSI 180 Query: 181 VGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAMEK 240 VGE+TL IDHC+LVS +TD I TVYSHPQPFQQCS++L+RYPHW IEYT+STS+AMEK Sbjct: 181 VGELTLPIDHCVLVSTSTDAQQITTVYSHPQPFQQCSQYLSRYPHWNIEYTDSTSSAMEK 240 Query: 241 VAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTTL 300 VAQAKSP VAALGSEAGG L+GLQVLE +ANQ QN TRF+VLARKA+ VSDQVPAKTTL Sbjct: 241 VAQAKSPTVAALGSEAGGALHGLQVLEHCQANQTQNITRFLVLARKAVEVSDQVPAKTTL 300 Query: 301 LMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKALK 360 LMATGQQAGALVEALLVLRNHNLIMT+LESRPIHGNPWEEMFYLDIQANLES M+KALK Sbjct: 301 LMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGNPWEEMFYLDIQANLESLPMRKALK 360 Query: 361 ELGEITRSMKVLGCYPSENVVPVDP 385 EL EITRSMKVLGCY SENVVPVDP Sbjct: 361 ELAEITRSMKVLGCYASENVVPVDP 385 Lambda K H 0.318 0.132 0.374 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: 495 Number of extensions: 7 Number of successful extensions: 1 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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