Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_011317857.1 AVA_RS05095 imidazole glycerol phosphate synthase subunit HisF
Query= BRENDA::Q9SZ30 (592 letters) >NCBI__GCF_000204075.1:WP_011317857.1 Length = 257 Score = 158 bits (399), Expect = 3e-43 Identities = 110/313 (35%), Positives = 162/313 (51%), Gaps = 59/313 (18%) Query: 280 LAKRVIACLDVRTNDKGDLVVTKGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEIS 339 L+KR++ CLDV+ V KG N ++++ G PV+LA Y GADE+ Sbjct: 2 LSKRILPCLDVKAGR-----VVKG--------VNFVDLKDAGDPVELAKVYNDAGADELV 48 Query: 340 FLNITGFRDFPLGDLPMIQVLRQTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFR 399 FL+IT + +I V+ +T++ VF+PLTVGGGI+ SLE R Sbjct: 49 FLDITATHE---DRDTIIDVVYRTAEQVFIPLTVGGGIQ-----------SLENVKALLR 94 Query: 400 SGADKISIGSDAVSAAEEFIKSGVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDV 459 +GADK+SI S AV E +++ S +GNQ +VV+ID RR Sbjct: 95 AGADKVSINSAAVRDPE------------LIDRASDRFGNQCIVVAIDARR--------- 133 Query: 460 PYKVIRVTNPGPNGEEYAWYQCTVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQ 519 RV P + Y V GGRE + A AK VE+ GAGE+L+ +D DG Sbjct: 134 -----RVDPSNPGWDVY------VRGGRENTGLDALSWAKEVEKRGAGELLVTSMDADGT 182 Query: 520 GKGFDIDLVKLISDSVGIPVIASSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSV 579 G+D++L + I++SV IPVIAS GAG +H + A AAL A + H ++ + + Sbjct: 183 QAGYDLELTRAIAESVEIPVIASGGAGNCEHIYTALTEGKAEAALLASLLHYGQLSVAEI 242 Query: 580 KEHLQEERIEVRI 592 K +L++ ++ VR+ Sbjct: 243 KNYLRDCQVPVRL 255 Lambda K H 0.317 0.135 0.391 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: 342 Number of extensions: 18 Number of successful extensions: 7 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: 592 Length of database: 257 Length adjustment: 30 Effective length of query: 562 Effective length of database: 227 Effective search space: 127574 Effective search space used: 127574 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: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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