Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043743254.1 AMB_RS02640 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000009985.1:WP_043743254.1 Length = 415 Score = 356 bits (913), Expect = e-102 Identities = 189/391 (48%), Positives = 258/391 (65%), Gaps = 3/391 (0%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 TI +D++GKRV++R D NVP KDG V D TRI + T+ +GAKVI+L+H GRPK Sbjct: 4 TIDKLDVQGKRVLVRADLNVPAKDGKVTDTTRIDRSAATLIQLAAKGAKVIVLTHFGRPK 63 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G ++S + + L++ +GK V + +G +V+K + +K+G++ LLEN RFHP E Sbjct: 64 GRED-KYSQKLLVEPLAKAVGKAVAWADDCIGPDVEKLIASMKDGDIALLENVRFHPEEE 122 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184 KNDP AK A+L D +VNDAF TAHRAHAS G+A +P+ AG LM+ E++ L K Sbjct: 123 KNDPAFAKALAALGDAYVNDAFSTAHRAHASTEGLAHLLPAAAGRLMQAELEALGKALEA 182 Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244 PEKP ++GGAKVS K+ ++ NL+ K D ++IGG M TFL A GK+VG S E+D D Sbjct: 183 PEKPVAAIVGGAKVSTKLDLLGNLVSKVDYLIIGGGMANTFLFAQGKQVGKSLCEKDLAD 242 Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELF 304 A+ +LEKAKE IVLPVDAV+A + +VV + D +P M LD GP + E Sbjct: 243 TARAILEKAKEAKCHIVLPVDAVVAGEFAENAANEVVSV-DAVPADKMILDAGPASAEAI 301 Query: 305 KQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKG-AITVVGGGDSAAAVNKF 363 +L KT+VWNGP+G FEI F + T VA A T +G +TV GGGD+ +A+ K Sbjct: 302 IDRLGGCKTLVWNGPLGAFEIAPFDKATNAVAQWAAERTLQGKLLTVGGGGDTVSALAKA 361 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G+E+KFS++ST GGA LE+LEGKELPG+A++ Sbjct: 362 GVEEKFSYISTAGGAFLEWLEGKELPGVAAL 392 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: 674 Number of extensions: 30 Number of successful extensions: 4 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: 415 Length adjustment: 35 Effective length of query: 619 Effective length of database: 380 Effective search space: 235220 Effective search space used: 235220 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