Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011187346.1 DP_RS00500 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000025945.1:WP_011187346.1 Length = 392 Score = 371 bits (953), Expect = e-107 Identities = 191/392 (48%), Positives = 270/392 (68%), Gaps = 6/392 (1%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63 ++R+++L GKRV++RVDFNVP+ D + DD RIR LPT++Y LEQG ++I+ SH+GRP Sbjct: 3 SLRELELAGKRVLVRVDFNVPMDDKQRITDDIRIRMVLPTLRYVLEQGGRLIICSHMGRP 62 Query: 64 KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 KG+ E+SLAP+A+ L+ LLG++V P +G EV+ V L GEVLLL+N RF+ E Sbjct: 63 KGKRVEEYSLAPIARHLAGLLGRDVGIAPDCIGAEVEAQVAALGVGEVLLLQNLRFYGEE 122 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKVT 182 T+ND A A LAD++VNDAF +HRAHAS VG+A+ + AGFL++ EI + K Sbjct: 123 TENDAVFAGKLAGLADVYVNDAFAVSHRAHASVVGVAERVAEKCAGFLLQTEIDYFHKSM 182 Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242 +P +P V ++GGAKVS KIG + N++ K D+++IGGAM TFL + G +VG+S+VE+D Sbjct: 183 NDPIRPLVALVGGAKVSSKIGALENMLGKVDKMIIGGAMANTFLMSQGVDVGASKVEDDL 242 Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302 + A+ L+ A E+G+++ LPVD V+A + K V D +PEGWM LD+GP + Sbjct: 243 LVTARNFLQAAGERGMKVYLPVDFVVADRFAADAVHKTVPA-DSVPEGWMALDVGPASSI 301 Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362 LF++ L A T+VWNGPMG FE+D FA GT + +AA A+++ GGGDS AAV K Sbjct: 302 LFREALQGAGTIVWNGPMGAFEMDAFAGGTMSLCRDVAA---SQALSITGGGDSNAAVKK 358 Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G D S++STGGGA L+ +EGK LPG+ ++ Sbjct: 359 SGEADNISYMSTGGGAFLQLMEGKTLPGVDAL 390 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: 634 Number of extensions: 38 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: 392 Length adjustment: 34 Effective length of query: 620 Effective length of database: 358 Effective search space: 221960 Effective search space used: 221960 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