Align candidate WP_011736451.1 PPRO_RS12800 (DUF4445 domain-containing protein)
to HMM PF14574 (RACo_C_ter)
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/PF14574.10.hmm # target sequence database: /tmp/gapView.19553.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: RACo_C_ter [M=261] Accession: PF14574.10 Description: C-terminal domain of RACo the ASKHA domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-63 198.3 0.0 1.3e-62 197.3 0.0 1.5 2 lcl|NCBI__GCF_000015045.1:WP_011736451.1 PPRO_RS12800 DUF4445 domain-cont Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736451.1 PPRO_RS12800 DUF4445 domain-containing protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.0 0.0 0.17 0.17 154 172 .. 74 92 .. 63 94 .. 0.78 2 ! 197.3 0.0 1.3e-62 1.3e-62 3 249 .. 168 413 .. 166 415 .. 0.95 Alignments for each domain: == domain 1 score: -3.0 bits; conditional E-value: 0.17 RACo_C_ter 154 LleevglevedidkvylaG 172 ++ +g++++ +++v +aG lcl|NCBI__GCF_000015045.1:WP_011736451.1 74 VCGDAGVAWDLVERVAIAG 92 5667888899999999998 PP == domain 2 score: 197.3 bits; conditional E-value: 1.3e-62 RACo_C_ter 3 slliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignekp 71 sl++D+GTN+E++l + ++a+saaaGPA+EGg+++cGm A +gAi++v+i+++ v+ +vign p lcl|NCBI__GCF_000015045.1:WP_011736451.1 168 SLFLDLGTNGEMALVAGETVWATSAAAGPAFEGGNLSCGMAALSGAISSVRIEHDR--VRTEVIGNVLP 234 89***************************************************999..*********** PP RACo_C_ter 72 kGicGsGiidliaelleagiidkkgklnkel.....kserireeeeteeyvlvlaeesetekdivitek 135 GicGsG++++i++l+++gi++ g+l+++ r+ ++++++++v++ + ++ +++t++ lcl|NCBI__GCF_000015045.1:WP_011736451.1 235 LGICGSGVLEAITQLVQHGILEPGGRLRDSSeissnLAGRVVSHDGENAFVIHRDA----QRMLLLTQS 299 ***************************887644433456889999999***98875....468****** PP RACo_C_ter 136 DidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNts 204 Di++++ ak+Ai+ag+++L +++g++ + +++v l+G+fG+++ +e t+G++ ++++++ ++ lcl|NCBI__GCF_000015045.1:WP_011736451.1 300 DIRQVQLAKGAIRAGLEVLFHRAGISPSGLSSVRLTGSFGAVVRPEWLKTVGIFDASMVHTIVFTPEGA 368 ********************************************************************* PP RACo_C_ter 205 lagAraallsreareeleeiarkityielavekkFmeefvaalfl 249 lagA+ l+ ++ +e +e++a + + + l+ ++ F++ f+++l + lcl|NCBI__GCF_000015045.1:WP_011736451.1 369 LAGAERSLMRPDGFEAVERLALRFRVVPLSGTPLFERLFLRSLEF 413 ***************************************998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (416 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 14.34 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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