Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012965628.1 FERP_RS05615 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000025505.1:WP_012965628.1 Length = 405 Score = 232 bits (592), Expect = 2e-65 Identities = 155/400 (38%), Positives = 229/400 (57%), Gaps = 34/400 (8%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 T+ D+ GK+V++RVD N P+ + + D TR + T+K LE A V +L+H RP Sbjct: 7 TLDDIQYSGKKVLLRVDINSPIVESRILDTTRFESHYETLK-ELENSA-VAILAHQSRPG 64 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 + +L A+ L ++G+EV+++ + V K V+ LK GE++LLEN RF+ E Sbjct: 65 KDDFT--TLEAHAEVLERIVGREVEYLDEIFSSCVIKRVKRLKPGEIVLLENVRFYSEEQ 122 Query: 125 -KNDPE------LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKF 177 K PE + + A L D++VNDAF +HR HAS +G +PSVAG L+EKE+K Sbjct: 123 LKRSPEEHANCIMVRKLAPLFDLYVNDAFSASHRPHASLIGFPPVMPSVAGRLVEKEVKA 182 Query: 178 LSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEK--ADRILIGGAMMFTFLKALGKEVGS 235 LSK E + +LGGAK+ D + V+ N++E AD++ + G + FLK G ++G Sbjct: 183 LSK-ALRSEGRKIFILGGAKIEDSVKVLKNVLENGIADKVALTGVVANYFLKLSGFKLGE 241 Query: 236 SR---VEEDKIDL----AKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIP 288 +EE+K + K+LLEK K+K I+LPVD I+ E++ V++++ Sbjct: 242 ENEKIIEENKDGVNDEEMKKLLEKYKDK---IILPVDVA----IDANGEREDVKLEEF-- 292 Query: 289 EGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAI 348 +G M DIG ETI + +++ V NGP GVFE + FA GT +V A+A K Sbjct: 293 KGGMIKDIGFETISMLAEEIPKYDIAVINGPAGVFEEEAFATGTAEVLKAVA----KAGY 348 Query: 349 TVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKEL 388 +VVGGG A A FG+ K H+STGGGAS+ FL G+ L Sbjct: 349 SVVGGGHIATAARLFGIARKIDHISTGGGASIRFLSGESL 388 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: 639 Number of extensions: 36 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: 654 Length of database: 405 Length adjustment: 35 Effective length of query: 619 Effective length of database: 370 Effective search space: 229030 Effective search space used: 229030 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 Apr 10 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