Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011867822.1 MMARC5_RS00230 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000016125.1:WP_011867822.1 Length = 414 Score = 242 bits (617), Expect = 3e-68 Identities = 157/417 (37%), Positives = 238/417 (57%), Gaps = 36/417 (8%) Query: 4 MTIRDVDLKGKRVIMRVDFNVP--VKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLG 61 +T+ D +L+GK V +RVD N P V G + DDTRI+A TI ++GAKV++L+H Sbjct: 3 LTLDDFELEGKTVALRVDINSPIDVNTGDILDDTRIKACYDTITGLSKKGAKVVILAHQS 62 Query: 62 RPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHP 121 RP + +L AK+LSE+L EV V ++ + A+ + GE++LLEN R Sbjct: 63 RPGKKDFT--TLEAHAKKLSEVLNMEVTHVDGLICASARDAILSMDNGEIILLENVRLLA 120 Query: 122 GETKND--------PELAKFWASLADIH------VNDAFGTAHRAHASNVGIAQFIPSVA 167 E +D PE + +H VNDAF AHRA S VG + ++P + Sbjct: 121 EEVLSDWKSWEAITPEKQAKTVMIKKLHPFFDYFVNDAFAAAHRAQPSLVGFSYYVPMLC 180 Query: 168 GFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEK--ADRILIGGAMMFTF 225 G +MEKE+ L+KV NPE+P V LGGAK D I V+ N++EK AD++L G + F Sbjct: 181 GRVMEKELFTLTKVLKNPERPCVFALGGAKADDSIEVLKNVLEKQTADQVLTSGVVANIF 240 Query: 226 LKALGKEVG------SSRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKK 279 L A G ++G + +I++AKEL+ K +K IV+P+DA + ++ +K Sbjct: 241 LVAKGYKIGPNENLIADMGYTGQIEIAKELISKYGDK---IVVPIDAGL--NVDGERVEK 295 Query: 280 VVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAI 339 + I++ I D+G T++L+++ L +AKT+V NGP GVFE +F +GT+++ ++ Sbjct: 296 ELDINEEITHPIH--DMGENTMKLYEEILKNAKTIVANGPAGVFENKNFLKGTEELLKSV 353 Query: 340 AALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD 396 A +V+GGG +AA GL K H+STGGGA +EFL GK+LP I +++ Sbjct: 354 A---NSEGFSVIGGGHLSAAAEVVGLAGKMGHISTGGGACIEFLAGKKLPVIEMLSE 407 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: 645 Number of extensions: 38 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: 414 Length adjustment: 35 Effective length of query: 619 Effective length of database: 379 Effective search space: 234601 Effective search space used: 234601 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