Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 3607885 Dshi_1293 glucosamine--fructose-6-phosphate aminotransferase, isomerizing (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4831 (340 letters) >FitnessBrowser__Dino:3607885 Length = 606 Score = 119 bits (299), Expect = 2e-31 Identities = 101/308 (32%), Positives = 147/308 (47%), Gaps = 18/308 (5%) Query: 45 VARGSSDHAASYFAYLTMQLLGIPVASLPMSVVTMQQAPLKVSGQVAFAFSQSGQSPDLV 104 VA G++ +A Y QL G+PV S + P+ F SQSG++ D + Sbjct: 295 VACGTAFYACQTAKYWFEQLTGLPVDIDIASEFRYRSPPIGPRTAALFV-SQSGETADTL 353 Query: 105 NSLRLLRKRGALSISLVNAEDSPLEAACEFSLPLCAGTESSVAATKSFIATLSA------ 158 +LR + +S+ N S + +LP AG E VA+TK+F L+ Sbjct: 354 AALRYCAGKADHILSICNVPQSSIARESTVALPTLAGVEIGVASTKAFTCQLTVLALLAL 413 Query: 159 -SARLIGHWKEDT--ELLDACRALPEGLRDAAQQDWS--QAIDALRDCQRLMVIGRGAGF 213 +AR GH + T E L A R LP L A Q+ L + + ++ +GRGA + Sbjct: 414 HAARQRGHCDDATLAEHLTALRGLPGLLNLALGQEAEIETVSRELAEARDILFLGRGAMY 473 Query: 214 AIAQEAALKFKETSAIQAEAFSSAEVRHGPMALIGDNYPLLVFAPRGAEQAGLLSLAADM 273 IA E ALK KE S I AE ++S E++HGP+AL+ P++VFAP +S ++ Sbjct: 474 PIALEGALKLKEISYIHAEGYASGELKHGPIALVDPAVPVIVFAPTDPLFDKTVSNMQEV 533 Query: 274 RQRGALVLLAAPDDVLER----DLTLTRAEH--PALDPILAIQSFYVMAAGLAVARGMDP 327 R VLL + L+ + H P L PIL ++A AVA+G D Sbjct: 534 MARQGKVLLVSDATGLDTAGPGSWATIQMPHVSPFLAPILYAIPAQLLAYHTAVAKGTDV 593 Query: 328 DQPRHLSK 335 DQPR+L+K Sbjct: 594 DQPRNLAK 601 Lambda K H 0.319 0.131 0.366 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: 412 Number of extensions: 13 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: 340 Length of database: 606 Length adjustment: 33 Effective length of query: 307 Effective length of database: 573 Effective search space: 175911 Effective search space used: 175911 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 (21.8 bits) S2: 51 (24.3 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