Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008990092.1 I215_RS01065 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000300875.1:WP_008990092.1 Length = 396 Score = 380 bits (975), Expect = e-110 Identities = 193/395 (48%), Positives = 273/395 (69%), Gaps = 4/395 (1%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63 TI D + K+ ++RVDFNVP+ D V D TRI AA PTI LE+G IL+SHLGRP Sbjct: 3 TIEDFNFNNKKALIRVDFNVPLDGDFNVTDTTRIEAAKPTIVKVLEEGGSAILMSHLGRP 62 Query: 64 KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 KG+ S E SL + ++SE++G +VKFV +G + ++A ++L+ GEVLLLEN RFH E Sbjct: 63 KGKKSDELSLKHIVAKVSEIIGVQVKFVDQSIGKDAEQAAKDLQPGEVLLLENLRFHSEE 122 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS--VAGFLMEKEIKFLSKV 181 + A+ + L D++VNDAFGTAHRAHAS +A++ G+L+ KEI+ ++KV Sbjct: 123 EAGEESFAEALSKLGDVYVNDAFGTAHRAHASTTIVAKYFGQNKCFGYLLAKEIEAIAKV 182 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 + EKP +LGG+KVS KI +I N+++K D ++IGG M +TF+KA G ++G S E+D Sbjct: 183 MESGEKPVTAILGGSKVSSKITIIENILDKVDHLIIGGGMTYTFIKAQGGKIGDSICEDD 242 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301 K +LA +L+ A+ KGV++ LPVD + A + ++V + + IP+GW GLD GP+T+ Sbjct: 243 KQELALRILKDAQAKGVKVHLPVDVLAANDFNNDADTQIVDVKE-IPDGWQGLDAGPKTL 301 Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361 E FK+ + ++KT++WNGP+GVFE+ FA+GT + I T+ GA ++VGGGDS AAV Sbjct: 302 ENFKEVILESKTILWNGPIGVFEMPSFAKGTIAIGNYIDQATKDGAFSLVGGGDSVAAVK 361 Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD 396 +FG EDK S+VSTGGGA LE LEGK LPGIA+I + Sbjct: 362 QFGFEDKVSYVSTGGGAMLESLEGKTLPGIAAILE 396 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: 652 Number of extensions: 37 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: 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 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