Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 6938654 Sama_2757 phosphoglycerate kinase (RefSeq)
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__SB2B:6938654 Length = 393 Score = 338 bits (866), Expect = 3e-97 Identities = 187/396 (47%), Positives = 258/396 (65%), Gaps = 12/396 (3%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKRV++R D NVPV DGVV D R+RA+LPTIK ALE+GA V+++SHL Sbjct: 1 MTIIKMSDLDLNGKRVLIREDLNVPVADGVVTSDARLRASLPTIKLALEKGAAVMVMSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE + EFS+ PV L+ L V+ V + D V AV GEV++ EN RF Sbjct: 61 GRPTEGEYNEEFSMKPVVNYLTAALDCPVRLVSDYL-DGVDVAV-----GEVVVFENVRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE KND L+K A+L D++V DAFGTAHRA AS G+ + P + AG L+ E+ L Sbjct: 115 NKGEKKNDEALSKKMAALCDVYVMDAFGTAHRAEASTNGVGLYAPIACAGPLLAAELDAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K NP +P V ++GG+KVS K+ V+ +L D++++GG + TF+ A G +VG S Sbjct: 175 GKALDNPARPLVAIVGGSKVSTKLTVLESLSGIVDQLVVGGGIANTFIAAAGNQVGKSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D ID AK L+ A+ +G +I +P D V+ ++ P + + D + M DIGP Sbjct: 235 EADLIDEAKRLVANAQSRGGDIPVPTDVVVGKEFSPTAVATLKNVSD-VAADDMIFDIGP 293 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 ++ E L +A T+VWNGP+GVFE D F EGTK++A AIA E A ++ GGGD+ A Sbjct: 294 DSAEALAAILKNAGTIVWNGPVGVFEFDQFGEGTKRIAQAIA---ESSAFSIAGGGDTLA 350 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 AV+K+G+ DK S++STGGGA LEFLEGKELP +A + Sbjct: 351 AVDKYGIADKVSYISTGGGAFLEFLEGKELPAVAML 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: 617 Number of extensions: 38 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: 393 Length adjustment: 34 Effective length of query: 620 Effective length of database: 359 Effective search space: 222580 Effective search space used: 222580 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