Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate AZOBR_RS06155 AZOBR_RS06155 6-phosphofructokinase
Query= CharProtDB::CH_024070 (320 letters) >FitnessBrowser__azobra:AZOBR_RS06155 Length = 361 Score = 208 bits (530), Expect = 1e-58 Identities = 130/333 (39%), Positives = 191/333 (57%), Gaps = 35/333 (10%) Query: 3 KKIGVLTSGGDAPGMNAAIRGVV-RSALTEGLEVMGIYDGYLGLYEDRMVQ---LDRYSV 58 K+IG+LTSGGD G+NA IR VV R+ LT G +V+GI +G GL + R VQ LD V Sbjct: 5 KRIGILTSGGDCAGLNAVIRAVVHRAVLTYGWQVLGIKEGTQGLLQ-RPVQYQVLDLPQV 63 Query: 59 S-DMINRGGTFLGSAR--------FPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMG 109 +M+ GGT LG+ + ++ I ++ G+DAL+ IGGDGS+ Sbjct: 64 DGNMMRMGGTILGTTNRGDPFAYPMADGTQKDRSDEIIGGYRELGLDALIGIGGDGSFAI 123 Query: 110 AMRLTEMG-FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVE 168 +L + G F +G+P TIDND+ T+ ++G+ TA+ VEA+DRL+ T++SH R+ V+E Sbjct: 124 LKKLADKGGFQMVGIPKTIDNDLGLTEVSVGYDTAVGVAVEALDRLQPTAASHARVMVLE 183 Query: 169 VMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDV 228 VMGR G + LAA IAGG + V++PE+ +S E + +IK + G+ A+V ++E + V Sbjct: 184 VMGRDAGHIALAAGIAGGADVVLIPEIAYSIEKIAQKIKQVRSTGRNFALVVVSEAVKTV 243 Query: 229 --------------------DELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRM 268 D + I + TG ETR TVLGH+QRG P P DR++AS Sbjct: 244 DGTGVQKLFQGGQKRYGGIGDYIGEKIAEATGAETRVTVLGHVQRGSMPSPRDRLVASAF 303 Query: 269 GAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDAI 301 G +A+DL+ G R V + ++ I +AI Sbjct: 304 GVHAVDLIAEGKFDRMVAWSDRGVIDVPITEAI 336 Lambda K H 0.322 0.141 0.413 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: 380 Number of extensions: 23 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: 320 Length of database: 361 Length adjustment: 28 Effective length of query: 292 Effective length of database: 333 Effective search space: 97236 Effective search space used: 97236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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