Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_057509308.1 ABB28_RS14530 SIS domain-containing protein
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_001431535.1:WP_057509308.1 Length = 342 Score = 406 bits (1044), Expect = e-118 Identities = 216/341 (63%), Positives = 250/341 (73%), Gaps = 3/341 (0%) Query: 23 APASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFAR 82 APA T MFREA EAA V A Q N ++ LA LRA PP VVTCARGSSDHAAT+A+ Sbjct: 5 APADTLMFREAAEAADVIAAQFARNHGVMETLAASLRAAPPPFVVTCARGSSDHAATYAK 64 Query: 83 YLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLAAVKAAKAAGAHAV 142 YL+ET+ G++ +SA PSV SVY A+ +L GAL++ ISQSGKSPDLL +AAKAAGA V Sbjct: 65 YLLETQLGLVVASASPSVGSVYAAALHLRGALFIVISQSGKSPDLLRNAEAAKAAGARVV 124 Query: 143 ALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAAWTEDAELTAALQD 202 ALVNV DSPLA LAD V+PLHAG E SVAATKSY+A+L AV QL A W +D+ L AAL Sbjct: 125 ALVNVEDSPLAQLADTVLPLHAGAERSVAATKSYLASLAAVLQLAAYWKQDSALRAALDA 184 Query: 203 LPTALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAE 262 LP AL AW DWS E L ASNL+VLGRG+G G A EAALKFKETCGLHAEA+S+AE Sbjct: 185 LPAALRQAWQADWSTVTEGLVEASNLFVLGRGLGLGAAQEAALKFKETCGLHAEAYSSAE 244 Query: 263 VLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGGGGDAPDALPTLAS 322 V HGPMALV GFP L FAQ DE+ A +A ARGA V +AG GGD P A A Sbjct: 245 VKHGPMALVGPGFPVLAFAQPDETGAGTRAVADEFAARGAQVWLAGAGGDLPVA---AAP 301 Query: 323 HPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVTETI 363 HP+ P+L +QSFYR NAL++ RG++PD PPHLNKVTET+ Sbjct: 302 HPLCAPLLTVQSFYRAINALALRRGHNPDLPPHLNKVTETV 342 Lambda K H 0.315 0.128 0.360 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: 386 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: 363 Length of database: 342 Length adjustment: 29 Effective length of query: 334 Effective length of database: 313 Effective search space: 104542 Effective search space used: 104542 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: 49 (23.5 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