Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_068461577.1 APY04_RS08280 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_001541235.1:WP_068461577.1 Length = 402 Score = 368 bits (944), Expect = e-106 Identities = 193/391 (49%), Positives = 260/391 (66%), Gaps = 2/391 (0%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 +I DVD+ GKRV++R D NVPV DG V D TR+ L +K ++GA+V+++SH GRPK Sbjct: 8 SIADVDVAGKRVLVRADLNVPVADGKVSDATRLERILDGLKDLSQRGARVVVISHFGRPK 67 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G P+PE SLAPVA +L ELLGK V FVPA +GDE + AV L+ G + +LEN RFH GE Sbjct: 68 GAPNPEMSLAPVAAKLGELLGKPVTFVPACIGDEAESAVAALQPGAIAVLENLRFHAGEE 127 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184 KND A D++VNDAF AHRAHAS G+A+ +P+ AG LM +EI L V N Sbjct: 128 KNDDAFVAALARSGDLYVNDAFSAAHRAHASTEGLARVLPAYAGPLMIEEINALRAVLEN 187 Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244 P++P ++GGAKVS KI ++ +L+ K D+++IGG M TFL + G +VG S E D ++ Sbjct: 188 PQRPVAALVGGAKVSSKIPILKHLIGKVDKLIIGGGMANTFLMSHGVDVGRSLAEPDLLE 247 Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304 A+E++ AK +VLP D VIA++ + GV VV I +P M LD+GP +IE Sbjct: 248 TAREIMAAAKAHNCAVVLPEDVVIAREFKSGVANAVVPI-LAVPSDAMILDVGPRSIEHN 306 Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKG-AITVVGGGDSAAAVNKF 363 L + +T++WNGPMG FEI F EGT +A A LT +G +TV GGGD+ AA+N Sbjct: 307 CAVLKECRTLLWNGPMGAFEISPFGEGTFGLAREAARLTREGKLVTVAGGGDTVAALNAA 366 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G F++VST GGA LE+LEG+ELPG+A++ Sbjct: 367 GATPDFTYVSTAGGAFLEWLEGRELPGVAAL 397 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: 613 Number of extensions: 26 Number of successful extensions: 3 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: 402 Length adjustment: 35 Effective length of query: 619 Effective length of database: 367 Effective search space: 227173 Effective search space used: 227173 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