Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011766565.1 AZO_RS14270 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000061505.1:WP_011766565.1 Length = 394 Score = 332 bits (850), Expect = 3e-95 Identities = 181/397 (45%), Positives = 261/397 (65%), Gaps = 12/397 (3%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSH 59 M+ + D+D++GK+V +R D NVP + G + +DTRIRA++P+I+Y L+ GA V++ SH Sbjct: 1 MQVKKLTDLDVRGKKVFIRADLNVPQDEAGNITEDTRIRASIPSIQYCLDNGAAVMVTSH 60 Query: 60 LGRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTR 118 LGRP +GE P+ +LAPVA RL +LL K VK + V + E+K GEV+LLEN R Sbjct: 61 LGRPTEGEVGPDDTLAPVAVRLGQLLHKPVKLIANWV-----EGGFEVKPGEVVLLENCR 115 Query: 119 FHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKF 177 + GE K++ ELAK A+L D++VNDAFGTAHRA A+ GIA+F P S AG LM EI Sbjct: 116 CNKGEKKDNEELAKKMAALCDVYVNDAFGTAHRAEATTHGIARFAPVSCAGILMGAEIDA 175 Query: 178 LSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSR 237 LSK + P +P V ++GGAKVS K+ ++ L +K D++++GG + TFL A GK +G S Sbjct: 176 LSKALHQPARPLVAIVGGAKVSTKLTILKTLADKVDQLIVGGGIANTFLLAAGKRIGESL 235 Query: 238 VEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIG 297 E + + A+++++ K +G E+ LP+D V+A ++ + +D+ P + LD G Sbjct: 236 AEPEMVREAQQVMDIMKSRGAEVPLPIDVVVADEVSALARANRISVDEVGPHDRI-LDFG 294 Query: 298 PETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSA 357 P+T ++ A T+VWNGP+GVFE FA GTK +A AIA A ++ GGGD+ Sbjct: 295 PKTSAKLADIIAHAGTIVWNGPVGVFEHAQFAGGTKMMASAIA---HSEAFSIAGGGDTL 351 Query: 358 AAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 AA+ KF + D ++STGGGA LEFLEGK+LP IA++ Sbjct: 352 AAIAKFHIADDVGYISTGGGAFLEFLEGKKLPAIAAL 388 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: 650 Number of extensions: 27 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: 394 Length adjustment: 34 Effective length of query: 620 Effective length of database: 360 Effective search space: 223200 Effective search space used: 223200 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