Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013460134.1 SULKU_RS06430 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000183725.1:WP_013460134.1 Length = 404 Score = 353 bits (907), Expect = e-102 Identities = 193/397 (48%), Positives = 267/397 (67%), Gaps = 9/397 (2%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGA-KVILLSHLGR 62 +++DVDL GKRV++RVDFNVP+ + DD+RIRAALPTI Y ++ A + L+SHLG+ Sbjct: 13 SLKDVDLAGKRVLIRVDFNVPMDAHYNISDDSRIRAALPTINYCIDHNACSITLISHLGQ 72 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 PK +SL + KRL LL K+V+F+ + D +K + LLEN RF G Sbjct: 73 PKNGYEDRYSLVHIQKRLERLLEKKVEFIDDL--DTLKAQNSHCSAERIFLLENIRFFQG 130 Query: 123 ETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKV 181 E KNDP K A L DI+VNDAFGT+HR AS GIA F VAGFLM +EI+ +K Sbjct: 131 EKKNDPAFCKQLADLCDIYVNDAFGTSHRKDASTYGIADFAKIKVAGFLMMREIEAFTKA 190 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 NP +P +V+GG+K+S KI ++T++M K D+++IGGAM TFLKAL ++ +S VE+D Sbjct: 191 LENPIRPIALVVGGSKISSKITLLTSVMPKIDKLIIGGAMSNTFLKALDHDMKASLVEDD 250 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301 I++AKE+L +AK GV++ LPVD VI IE V+ KV D + EG+ +DIGP T+ Sbjct: 251 FIEVAKEVLNEAKAHGVKVYLPVDVVITDSIESPVDIKVTPAQD-VLEGFHAVDIGPATL 309 Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361 +LF + + + T++WNGPMG++EI F++GT ++A IA + A ++VGGGD+A AV Sbjct: 310 KLFSEAIELSNTIIWNGPMGIYEISQFSKGTFKLASFIA---DSYAYSIVGGGDTADAVE 366 Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKK 398 K G ++KFS +STGGGASLE LEGK LPG + K+ Sbjct: 367 KAGEKEKFSFISTGGGASLELLEGKILPGFEKLDRKE 403 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: 634 Number of extensions: 41 Number of successful extensions: 7 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: 404 Length adjustment: 35 Effective length of query: 619 Effective length of database: 369 Effective search space: 228411 Effective search space used: 228411 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