Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_089136501.1 CES79_RS04995 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::pseudo3_N2E3:AO353_04455 (336 letters) >NCBI__GCF_002217945.1:WP_089136501.1 Length = 605 Score = 105 bits (263), Expect = 2e-27 Identities = 81/263 (30%), Positives = 137/263 (52%), Gaps = 13/263 (4%) Query: 82 VSGQAVFAF-SQSGQSPDLVNSLRLLRKRGALSISMVNAENSPLEAACEFSLPLCAGTES 140 +S + F F SQSG++ D L + G S+++ N +NS L ++L L AG E Sbjct: 338 LSKKPFFIFLSQSGETADSREVLVNVNAGGYESLTITNVQNSTLSREATYTLLLHAGPEI 397 Query: 141 SVAATKSFIATLSASARLI-AYWKQDPELL--------QAGLALP--EGLRDAATQDWSL 189 +VA+TK++ A ++ A L A + D +++ Q GL + L D ++ L Sbjct: 398 AVASTKAYTAQIAIEAILAKALGEADNQIVAQRFDVRHQLGLVATGMQALVDEKSKIEKL 457 Query: 190 AVDVLRDCQRLMVIGRGAGFAIAQEAALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPL 249 A IGRG ++++ EAALKLKE S +QAE F+S E+KHG +ALI+ P+ Sbjct: 458 AKASFLKTPNAFYIGRGIDWSVSLEAALKLKEISYVQAEGFASGELKHGTIALIEKGTPV 517 Query: 250 LVFAPRGAEQAGLLSLAAEMRQRGARVLLAAPDDVSERDLTLSRAE-HPALDPILAIQSF 308 + + S E RGA++L + +++ TL + P + P+L++ Sbjct: 518 IGIITQEKTAGLTRSNLQETMARGAQILTIVSESLAKPGDTLILPDVDPLMSPLLSVVPT 577 Query: 309 YVMAAGLAVARGMDPDQPRHLSK 331 ++A ++ +G+D D+PR+L+K Sbjct: 578 QLIAYYTSLNKGLDVDKPRNLAK 600 Lambda K H 0.318 0.130 0.362 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: 366 Number of extensions: 17 Number of successful extensions: 3 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: 336 Length of database: 605 Length adjustment: 33 Effective length of query: 303 Effective length of database: 572 Effective search space: 173316 Effective search space used: 173316 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 (21.8 bits) S2: 51 (24.3 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