Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate HSERO_RS03345 HSERO_RS03345 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__HerbieS:HSERO_RS03345 Length = 396 Score = 321 bits (822), Expect = 4e-92 Identities = 179/389 (46%), Positives = 248/389 (63%), Gaps = 13/389 (3%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP- 63 I + L+GKRV +R D NVP D G + +DTRIRA++P I+ A + GA V++ SHLGRP Sbjct: 10 ISNKQLQGKRVFIRADLNVPQDDAGNITEDTRIRASVPAIREAQQAGAAVMVTSHLGRPT 69 Query: 64 KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 +GE PE SLAPVAKRLSELLG EVK V V D V +++ G+V+LLEN R + GE Sbjct: 70 EGEFKPEDSLAPVAKRLSELLGSEVKLVANWV-DGV-----DVQPGQVVLLENCRLNKGE 123 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVT 182 KN ELA+ A L DI+VNDAFGTAHRA A+ G+A+F P + AG L+ E+ L K Sbjct: 124 KKNSDELAQKIAKLCDIYVNDAFGTAHRAEATTYGVAKFAPVACAGPLLAAELDALGKAL 183 Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242 P +P V ++ G+KVS K+ ++ L EK D +++GG + TF+ A G ++G S E D Sbjct: 184 NQPARPLVAIVAGSKVSTKLTILKTLAEKVDNLIVGGGIANTFMLAAGLKIGKSLAEPDL 243 Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302 +D AK +++ ++G + +P D V+ ++ P V D + + M DIGP+T Sbjct: 244 VDDAKAIIDLMAKRGASVPIPTDVVVGKEFSPTAAATVKAAAD-VADDDMIFDIGPQTAA 302 Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362 ++L A T+VWNGP+GVFE D F GT+ +A AIAA ++ GGGD+ AA+ K Sbjct: 303 ALAEQLGRAGTIVWNGPVGVFEFDQFGGGTETLARAIAA---SSGFSIAGGGDTLAAIAK 359 Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGI 391 + + DK ++STGGGA LEFLEGK LP + Sbjct: 360 YNIADKVGYISTGGGAFLEFLEGKTLPAV 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: 644 Number of extensions: 30 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: 396 Length adjustment: 34 Effective length of query: 620 Effective length of database: 362 Effective search space: 224440 Effective search space used: 224440 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 17 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