Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012537677.1 AFE_RS14895 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000021485.1:WP_012537677.1 Length = 401 Score = 346 bits (887), Expect = 1e-99 Identities = 189/404 (46%), Positives = 268/404 (66%), Gaps = 8/404 (1%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSH 59 M + + DV LKGKRV++R D NVP+ D G + DDTRIRA+LPTI+ AL GA+V+L+SH Sbjct: 1 MNVLRMMDVPLKGKRVLIREDLNVPMNDAGAITDDTRIRASLPTIRAALASGARVMLMSH 60 Query: 60 LGRPK-GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTR 118 LGRPK G + SLAPVA LS+LLG++V V + D K + +L++G+V++LEN R Sbjct: 61 LGRPKEGVFDEKASLAPVAAHLSQLLGRDVPLVRDWL-DAGKDRLAQLQDGDVVVLENVR 119 Query: 119 FHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKF 177 F+ GE+K+D L+K A+L D+ V DAFGTAHRA AS G+ +F P + AG L+ E+ Sbjct: 120 FNTGESKDDEALSKKMAALCDVFVMDAFGTAHRAQASTHGVGKFAPVACAGPLLVNELDA 179 Query: 178 LSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSR 237 L K NP +P V ++ G+KVS K+ ++ +L +K D++++GG + TF+ A G VG S Sbjct: 180 LGKALQNPRRPLVAIVAGSKVSTKLTILKSLADKVDQLVVGGGIANTFILAAGHSVGKSL 239 Query: 238 VEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIG 297 E D + A+ ++ A+ KG ++ LP D V+A+ + R+DD I M LDIG Sbjct: 240 CEADLVPDAQAIIAAARAKGGDVPLPSDVVVAKAFSETAPARTCRVDD-IAADDMVLDIG 298 Query: 298 PETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSA 357 P+T + L A T+VWNGP+GVFE D FA GT+ +A A+A E A ++ GGGD+ Sbjct: 299 PDTAKTLGDILRKAGTIVWNGPVGVFEFDAFAGGTEAIARAVA---ESSAFSIAGGGDTI 355 Query: 358 AAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKKIT 401 AA+NKF +EDK S++STGGGA LEFLEGK LP +A + ++ + T Sbjct: 356 AAINKFHIEDKVSYISTGGGAFLEFLEGKTLPAVAMLEERARGT 399 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: 612 Number of extensions: 29 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: 401 Length adjustment: 35 Effective length of query: 619 Effective length of database: 366 Effective search space: 226554 Effective search space used: 226554 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