Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_057687355.1 ABB28_RS15915 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_001431535.1:WP_057687355.1 Length = 391 Score = 329 bits (844), Expect = 1e-94 Identities = 179/396 (45%), Positives = 264/396 (66%), Gaps = 12/396 (3%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKRV++R D NVP+++G + + RI A+LPT+K ALEQGA V++ SHL Sbjct: 1 MSIVRMTDLDLSGKRVLIRQDLNVPIENGQISSEQRITASLPTLKRALEQGAAVMVTSHL 60 Query: 61 GRPK-GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRPK G+ S E SL PVA+RLSELLG++V + VG +++ G+++LLEN R Sbjct: 61 GRPKEGQWSEENSLQPVARRLSELLGRDVPLLRDWVGGV------DVQPGQIVLLENCRM 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGF-LMEKEIKFL 178 + GE K+D LA+ +A+L D+ V DAFGTAHRA AS G+ +F P AG L+ E+ L Sbjct: 115 NVGEGKDDEALARQYAALCDVFVMDAFGTAHRAQASTHGVIRFAPVAAGGPLLMAELDAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 +K P KP + ++ G+KVS K+ ++ +L+ K D++++GG + TF+ A G VG S Sbjct: 175 AKALKEPAKPLLAIVAGSKVSTKLELLASLVGKVDQLIVGGGIANTFIAAAGYPVGKSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D ++ AK+++ AK +G +I LP D V+A++ P E V + D + E + LDIGP Sbjct: 235 EPDLLETAKKIVADAKARGADIPLPTDVVVAKQFLPDAEATVKALAD-VAEDDLILDIGP 293 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 +T + + ++ A TVVWNGP+GVFE + F++GT+ +A AIA A ++ GGGD+ A Sbjct: 294 DTAQRYAALINQAGTVVWNGPVGVFEFEAFSKGTEALARAIAG---SRAFSIAGGGDTLA 350 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 AV+KF + S++STGGGA LEFLEGK LP +A++ Sbjct: 351 AVDKFDIAGDVSYISTGGGAFLEFLEGKTLPAVAAL 386 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: 608 Number of extensions: 28 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: 391 Length adjustment: 34 Effective length of query: 620 Effective length of database: 357 Effective search space: 221340 Effective search space used: 221340 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