Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_039106191.1 FPB0191_RS11165 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000807275.1:WP_039106191.1 Length = 386 Score = 317 bits (812), Expect = 6e-91 Identities = 180/401 (44%), Positives = 259/401 (64%), Gaps = 17/401 (4%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + ++D+DLKGKRV +R D NVPVK+G V D RIRA+LPTI+ A++QGAKV++ SH+ Sbjct: 1 MPIIKMQDLDLKGKRVFIRSDLNVPVKNGKVTSDARIRASLPTIELAIKQGAKVMVTSHI 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE +PE+SL PV L E + V+ V + D V E+KEGE+++LEN RF Sbjct: 61 GRPTEGEYNPEYSLQPVVDYLKEHVSYPVRLVKDYL-DGV-----EVKEGELVVLENVRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE K+D L+K +A+L DI+V DAFGTAHRA AS G+ F P S AG L+ E+ L Sbjct: 115 NKGEGKDDEALSKKYAALCDIYVMDAFGTAHRAQASTHGVGLFAPVSCAGPLLSAELDAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K NP +P V ++ G+KVS K+ V+ +L + AD+I++GG + TF+ A G VG S Sbjct: 175 GKALDNPARPMVAIVAGSKVSTKLTVLDSLSKVADQIIVGGGIANTFIAAEGYNVGKSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D I AK+L++ I +P D +A + + ++D + + LDIG Sbjct: 235 EADLIPEAKKLMQNC-----TIPVPTDVRVATEFSESATATLKSVND-VKDNEQILDIGD 288 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 + E + + +AKT++WNGP+GVFE +F GT+ VA AIA + ++ GGGD+ A Sbjct: 289 ASAEELAKIIKNAKTILWNGPVGVFEFPNFRRGTEIVAKAIA---DSAGFSIAGGGDTLA 345 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399 A++ FG+EDK S++STGGGA LEF+EGK+LP +A + + K Sbjct: 346 AIDLFGIEDKISYISTGGGAFLEFVEGKKLPAVAMLEARGK 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: 592 Number of extensions: 30 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: 386 Length adjustment: 34 Effective length of query: 620 Effective length of database: 352 Effective search space: 218240 Effective search space used: 218240 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