Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013451712.1 CALNI_RS08040 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000183405.1:WP_013451712.1 Length = 388 Score = 390 bits (1002), Expect = e-113 Identities = 200/388 (51%), Positives = 278/388 (71%), Gaps = 8/388 (2%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 ++ +D+KG+RV +RVDFNVP+K+GVV+DDTRI AL TI Y E+GAKVI+ SHLGRPK Sbjct: 4 SVESLDVKGRRVFLRVDFNVPIKNGVVKDDTRIVEALKTINYLKEKGAKVIMASHLGRPK 63 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 GE + E+SL PV++ S +KFV +G++V V ++K+G+V+LLEN RF+ GE Sbjct: 64 GEFNLEYSLKPVSEYFSAKFFP-IKFVDDCIGEKVHSTVNDMKDGDVILLENLRFYKGEE 122 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSV-AGFLMEKEIKFLSKVTY 183 KN PE + D++VNDAFGT HR HAS G+ + + AGFL++KE+++ K+ Sbjct: 123 KNLPEFSAALKEFTDVYVNDAFGTCHRKHASVFGLPELVEDKGAGFLVKKEVEYFEKLLK 182 Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243 +PEKP++ +LGGAKVSDKIGVI +L+ D I+IGGAM +TFLK LGK G S VE + + Sbjct: 183 SPEKPFIAILGGAKVSDKIGVIKSLINLVDEIIIGGAMAYTFLKFLGKNTGKSLVENEYL 242 Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303 + E ++ ++EKGV+I+LP+D V + + G + V +D IP+ MGLDIGP T+EL Sbjct: 243 GVVDETMKLSEEKGVKILLPIDHVCSDVFD-GEPEYVSGVD--IPDDLMGLDIGPATVEL 299 Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKF 363 F++++ AKT++WNGPMGVFE D++ +GT +A +AL GA+TVVGGGDS A+ K Sbjct: 300 FEKEVLKAKTILWNGPMGVFENDNYNKGTFAIA---SALASSGAVTVVGGGDSVNAIKKA 356 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGI 391 G+ DK SH+STGGGASLE++E LPGI Sbjct: 357 GVADKISHISTGGGASLEYIEFGSLPGI 384 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: 684 Number of extensions: 41 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: 388 Length adjustment: 34 Effective length of query: 620 Effective length of database: 354 Effective search space: 219480 Effective search space used: 219480 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