Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_018125210.1 B149_RS0110995 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000375485.1:WP_018125210.1 Length = 400 Score = 366 bits (939), Expect = e-105 Identities = 201/397 (50%), Positives = 268/397 (67%), Gaps = 10/397 (2%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKG 65 I +D+KGK+++ RVDFNVP+ + DD RIRA +PT++YA+EQGA VI+ +HLG+PKG Sbjct: 4 IDQMDIKGKKLLFRVDFNVPLDGSTITDDNRIRAVVPTLRYAMEQGAAVIVCAHLGKPKG 63 Query: 66 EPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFH---PG 122 + PE +LAP+AKRL ELL +V P VG +V+ L+ G+V++LEN RFH G Sbjct: 64 QVVPELTLAPIAKRLGELLETDVALAPDCVGPDVESMAASLQPGQVMMLENLRFHKEEQG 123 Query: 123 ETKND-PELAKFWASLADIHVNDAFGTAHRAHASNVGI-AQFIPSVAGFLMEKEIKFLSK 180 +T D + K ASLADI+VNDAFG AHRA+AS V + A GFLM+KE ++L Sbjct: 124 KTAEDRGDFGKQLASLADIYVNDAFGVAHRANASVVDVPAHAKDCCIGFLMKKEWEYLGT 183 Query: 181 VTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEE 240 +P++P+V V GGAKVS K+G++ NL+ K D I+IGGAM TFL A G VG S VE Sbjct: 184 ALADPKRPFVAVSGGAKVSSKLGILYNLLGKVDHIIIGGAMANTFLAAQGHGVGKSLVEN 243 Query: 241 DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRID-DGIPEGWMGLDIGPE 299 D D A +++E A++KG +I LP D V A P +K D IPE M LDIGPE Sbjct: 244 DLFDEALKIMETARQKGSQIHLPQDFVYAD--SPDADKANGSCGADCIPEDMMVLDIGPE 301 Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAA 359 +IE FK+ L A TVVWNGPMG+FE FAEG+ ++ +A + E A+T+VGGGD+ A Sbjct: 302 SIETFKKVLDGAGTVVWNGPMGLFETPAFAEGSMELCKVMADMPE--AVTIVGGGDTDAV 359 Query: 360 VNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD 396 V+K GL ++FS +STGGG+ LEFLEGKELP ++ + Sbjct: 360 VHKAGLTERFSFISTGGGSFLEFLEGKELPAFKALKE 396 Lambda K H 0.317 0.137 0.386 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: 623 Number of extensions: 35 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: 654 Length of database: 400 Length adjustment: 34 Effective length of query: 620 Effective length of database: 366 Effective search space: 226920 Effective search space used: 226920 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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