Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012676925.1 PERMA_RS01115 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000021565.1:WP_012676925.1 Length = 398 Score = 421 bits (1081), Expect = e-122 Identities = 219/394 (55%), Positives = 288/394 (73%), Gaps = 8/394 (2%) Query: 4 MTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 MT+ DVD+ GKRV +RVD+NVP+ + G + DDTRIR +PTI Y L++ AKVIL SHLGR Sbjct: 6 MTLEDVDVTGKRVFVRVDYNVPLDEHGHIVDDTRIRETIPTINYLLDKNAKVILASHLGR 65 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 PKGE +P++SL PVA+RL LL KEVKF P VG EV++ V +K+G+V+LLEN RFHPG Sbjct: 66 PKGERNPKYSLFPVARRLERLLNKEVKFAPDCVGKEVEELVFNMKDGDVVLLENLRFHPG 125 Query: 123 ETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKV 181 E NDPE AK A LA+I+V DAFGT HR HAS GI F+ P V GFL+E+E+K+ K Sbjct: 126 EEGNDPEFAKSLAKLAEIYVIDAFGTCHRKHASMYGIKDFVQPVVMGFLLERELKYFEKA 185 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 NP++P V +GG+KVS K+GVI +L++KAD+I IGGAM FTF+KA+G EVGSS VE+D Sbjct: 186 LVNPQRPVVAFIGGSKVSSKLGVIKHLLDKADKIFIGGAMAFTFIKAMGYEVGSSLVEDD 245 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRID-DGIPEGWMGLDIGPET 300 D A ++++AK++GV+ LPVD V Q I + V+ + IP+GWMGLDIG + Sbjct: 246 MFDEALYVIDEAKKRGVKFYLPVDFVCGQAISE--QTPVIEVAWQEIPKGWMGLDIGHAS 303 Query: 301 IELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAV 360 I L K+ L DA+T++WNGPMGVFEID F GT +A AIA E A+++ GGGD+ A+ Sbjct: 304 ITLIKEILKDAQTIIWNGPMGVFEIDKFKGGTFGLAHAIA---ESPALSIAGGGDTDYAI 360 Query: 361 NKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 +K G+ D+ S++STGGGA L+ LEGK LP + +I Sbjct: 361 HKAGVIDEISYISTGGGAFLKLLEGKVLPCLEAI 394 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: 659 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: 398 Length adjustment: 34 Effective length of query: 620 Effective length of database: 364 Effective search space: 225680 Effective search space used: 225680 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