Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_101443424.1 BD749_RS06020 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_002846395.1:WP_101443424.1 Length = 399 Score = 384 bits (986), Expect = e-111 Identities = 197/395 (49%), Positives = 273/395 (69%), Gaps = 8/395 (2%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVK-DGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63 T+ + GK+ ++RVDFNVP+ D + DDTRIRAA+PTI+ L G VIL+SHLGRP Sbjct: 3 TVDAYNFAGKKALVRVDFNVPLDADYRITDDTRIRAAVPTIQKILNDGGAVILMSHLGRP 62 Query: 64 KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123 K P ++SL + RLS+ VKF VG E + ++LK GE+LLLEN RFH E Sbjct: 63 KTGPEEKYSLRHLVDRLSKEFNTTVKFATDCVGPEAAQLAQDLKPGEILLLENLRFHKAE 122 Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS--VAGFLMEKEIKFLSKV 181 K D E A+ ++L D++VNDAFGTAHR HAS IA++ P+ V G++M E+ +V Sbjct: 123 EKGDLEFARELSTLGDVYVNDAFGTAHREHASTAVIARYFPNDKVMGYVMHAELDNARRV 182 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 N E+PY ++GGAK+SDKI +I LM+K D +LIGG M +TF+KA G E+GSS VEED Sbjct: 183 MDNAERPYTAIMGGAKISDKILIIEKLMDKVDNLLIGGGMSYTFVKADGGEIGSSLVEED 242 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKI--EPGVEKKVVRIDDGIPEGWMGLDIGPE 299 K++LA+ L+ A+EKGV +++PVD++IA + E V+ + I WMGLDIGP Sbjct: 243 KVELARRLIAMAREKGVNLMIPVDSIIADEFSNEANVD---TALSHHIKPLWMGLDIGPN 299 Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAA 359 E++ + ++KT++WNGPMGVFE+ +F+ GT+ VA A+ T +GA +++GGGDSAAA Sbjct: 300 AREMYADVIRNSKTILWNGPMGVFEMSNFSVGTEAVAEAVVDATRRGAYSLIGGGDSAAA 359 Query: 360 VNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 VN+ G D+ S+VSTGGGA LE++EGK LPG+A+I Sbjct: 360 VNQLGYADRVSYVSTGGGALLEYMEGKTLPGVAAI 394 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: 634 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 654 Length of database: 399 Length adjustment: 34 Effective length of query: 620 Effective length of database: 365 Effective search space: 226300 Effective search space used: 226300 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