Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011317630.1 AVA_RS03895 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000204075.1:WP_011317630.1 Length = 400 Score = 447 bits (1149), Expect = e-130 Identities = 228/399 (57%), Positives = 293/399 (73%), Gaps = 7/399 (1%) Query: 1 MEKMTIRDV---DLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVIL 56 M K T+ + D+ GKR ++RVDFNVP+ D G + DDTRIRAALPTI+ ++GAKVIL Sbjct: 1 MSKKTVASLSAADISGKRALVRVDFNVPLDDQGNITDDTRIRAALPTIQDLTQKGAKVIL 60 Query: 57 LSHLGRPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLEN 116 SH GRPKG + L PVAKRLSELLG+EV +GDEV V L+ G+VLLLEN Sbjct: 61 ASHFGRPKGVDE-KLRLTPVAKRLSELLGQEVVKTDDSIGDEVAAKVAALQNGQVLLLEN 119 Query: 117 TRFHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEI 175 RF+ E KNDPE AK A+ AD +VNDAFGTAHRAHAS G+ +F+ PSVAG+L+EKE+ Sbjct: 120 VRFYKEEEKNDPEFAKKLAANADFYVNDAFGTAHRAHASTEGVTKFLSPSVAGYLVEKEL 179 Query: 176 KFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGS 235 ++L NP++P ++GG+KVS KIGVI L+EK D+++IGG M+FTF KA G VG Sbjct: 180 QYLQSAIENPQRPLAAIIGGSKVSSKIGVIETLLEKCDKLIIGGGMIFTFYKARGLNVGK 239 Query: 236 SRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLD 295 S VEEDK++LAK L KAKE+GV ++LP D V+A P + V ID+ IP+GWMGLD Sbjct: 240 SLVEEDKLELAKSLEAKAKERGVSLLLPTDVVLADNFAPDANSQTVSIDN-IPDGWMGLD 298 Query: 296 IGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGD 355 IGP+++++F++ L+D KTV+WNGPMGVFE D FA GT+ +A +A + + G T++GGGD Sbjct: 299 IGPDSVKVFQEALADTKTVIWNGPMGVFEFDKFAAGTEAIAHTLAEIGKTGTTTIIGGGD 358 Query: 356 SAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 S AAV K GL D+ SH+STGGGASLE LEGK LPGIA++ Sbjct: 359 SVAAVEKVGLADQMSHISTGGGASLELLEGKVLPGIAAL 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: 707 Number of extensions: 36 Number of successful extensions: 5 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: 400 Length adjustment: 34 Effective length of query: 620 Effective length of database: 366 Effective search space: 226920 Effective search space used: 226920 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