Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043532756.1 JH15_RS17385 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000759345.1:WP_043532756.1 Length = 387 Score = 347 bits (890), Expect = e-100 Identities = 190/396 (47%), Positives = 267/396 (67%), Gaps = 18/396 (4%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 + KMT D+DL G+RV++R D NVP+K+G V D R+RA LPTIK A E GAKV+L+SHL Sbjct: 3 VRKMT--DLDLAGQRVLIREDLNVPIKNGRVTSDARLRACLPTIKAAAEAGAKVMLMSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GEP+ EFSLAPVA+ L LL + V+ V + EL +GEV LLEN RF Sbjct: 61 GRPTEGEPADEFSLAPVAEHLGTLLDRPVRLV-----KDYLDYSPELADGEVALLENVRF 115 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSV-AGFLMEKEIKFL 178 + GE K+D LAK +A+L D++V DAFGTAHRA AS G+A+F P+ AG L+ +E++ L Sbjct: 116 NSGEKKDDEALAKRYAALCDVYVMDAFGTAHRAQASTHGVARFAPTACAGPLLAQELEAL 175 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K NP++P V ++GG+KVS K+ V+ L EK D++++GG + TF+ A G VG S Sbjct: 176 EKALANPKRPMVAIVGGSKVSTKLDVLNALAEKCDQLIVGGGIANTFIAAAGYNVGKSLY 235 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E+D +D A +EK V+I LP D V+A + + VV+ D + + M LD+GP Sbjct: 236 EKDLVDKASAFMEK-----VDIPLPTDVVVATEFSESAD-AVVKGVDHVNDEEMILDVGP 289 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 + E L +A T++WNGP+GVFEID F +GT+ +A AIAA A ++ GGGD+ A Sbjct: 290 MSAEKLGDLLKEAGTILWNGPVGVFEIDQFGQGTQSLAQAIAA---SSAFSIAGGGDTLA 346 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 A++K+G+ D+ S++STGGGA LE++EGK LP +A++ Sbjct: 347 AIDKYGIADQVSYISTGGGAFLEYVEGKTLPAVAAL 382 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: 570 Number of extensions: 28 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: 387 Length adjustment: 34 Effective length of query: 620 Effective length of database: 353 Effective search space: 218860 Effective search space used: 218860 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