Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011308470.1 MBAR_RS18885 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000195895.1:WP_011308470.1 Length = 413 Score = 255 bits (652), Expect = 2e-72 Identities = 161/409 (39%), Positives = 248/409 (60%), Gaps = 34/409 (8%) Query: 4 MTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 +T+ DV L KRV++RVDFN P+ D G + DD +I++ LPT++ +LE +KV+L+SH GR Sbjct: 11 LTMSDVVLDNKRVLVRVDFNSPMDDNGNILDDKKIKSHLPTLQ-SLEH-SKVVLMSHQGR 68 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 P E +L AK +ELLG+EV + + + A++ L +GE+LLLENTRF+ Sbjct: 69 PGDEDYT--TLEAHAKLATELLGREVTYEDDIFSSCARNAIKSLAQGEILLLENTRFNAE 126 Query: 123 ETKNDP-------ELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEI 175 E N P ++ K L D+ +NDAF +HR+ S VG + +PSVAG LM+KEI Sbjct: 127 EITNRPPEKQAKSQMVKKLYPLFDLFINDAFSVSHRSQCSVVGFTEVLPSVAGILMDKEI 186 Query: 176 KFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEK--ADRILIGGAMMFTFLKALG--- 230 L K E P + +LGGAK +D I I+N++++ AD+IL G + F+ A+G Sbjct: 187 TGLDKALKCREHPAIFILGGAKANDSIKAISNILKRAGADKILTTGVVATIFMMAMGVDV 246 Query: 231 KEVGSSRVEE----DKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDG 286 EV +E+ D+I +A +LL K+ +I++P D + G E++ V +D Sbjct: 247 SEVNRKFIEDKKYMDQISIASKLL---KDYSGKIIVPQDVA----LNSGGERQEVEVDK- 298 Query: 287 IPEGWMGL-DIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEK 345 I +G + + DIG ETIE + + L +AK V++GP G+FE+D+F GT ++ A A + Sbjct: 299 IKKGNLPIADIGRETIENYSKYLKEAKLCVFHGPTGIFELDNFRLGTDELLKAAA----Q 354 Query: 346 GAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 + +V GGG + A+++ GL KFSH+S GGGAS+ ++ G+ LPGI ++ Sbjct: 355 ASYSVAGGGHTLDAIDQLGLGSKFSHISMGGGASITYISGEPLPGITAL 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: 595 Number of extensions: 41 Number of successful extensions: 8 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: 413 Length adjustment: 35 Effective length of query: 619 Effective length of database: 378 Effective search space: 233982 Effective search space used: 233982 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