Align candidate WP_028316647.1 G491_RS0126315 (hypothetical 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.20225.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-72 229.0 2.0 4.1e-72 228.5 2.0 1.2 1 lcl|NCBI__GCF_000429905.1:WP_028316647.1 G491_RS0126315 hypothetical prot Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028316647.1 G491_RS0126315 hypothetical protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 228.5 2.0 4.1e-72 4.1e-72 3 251 .. 277 517 .. 275 520 .] 0.95 Alignments for each domain: == domain 1 score: 228.5 bits; conditional E-value: 4.1e-72 RACo_C_ter 3 slliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek. 70 +lliD+GTN+E+ ++n+ +aas+a+GPA+EG+e+ cGm+A+pgAi+ v+i+ ++ +l+vig + lcl|NCBI__GCF_000429905.1:WP_028316647.1 277 ALLIDLGTNGELLFKNNGSFYAASCATGPAFEGAELDCGMQATPGAINGVKINGDQKVASLSVIGANGg 345 69**************************************************************64434 PP RACo_C_ter 71 ....pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyvlvlaeesetekdivitek 135 p GicG G+i+++ael+++g++++ g ++ ++ e+vl + ++ +++++i++k lcl|NCBI__GCF_000429905.1:WP_028316647.1 346 dgvqPAGICGPGVINALAELYRKGVVKSGGGFK-----------AGEREFVLFGGDPNNGNHSVYISQK 403 4445****************************3...........4789****9999999999******* PP RACo_C_ter 136 DidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAitiGllPdlelekvkqvGNts 204 Di++++ k+A+ +g+++Ll e+g + + +k+++aGafG++++ e+ i +G++Pdl+ ek++ +GN++ lcl|NCBI__GCF_000429905.1:WP_028316647.1 404 DIRSIQLGKGALATGIEFLLMEAG--LVQPEKILIAGAFGNHLNKEDIICLGMIPDLKSEKIEMAGNSA 470 ************************..8899*************************************** PP RACo_C_ter 205 lagAraallsreareeleeiarkityielavekkFmeefvaalflph 251 +agA +al+++ ++++ e+a+ki+ i+la + +F+++fv +l++p+ lcl|NCBI__GCF_000429905.1:WP_028316647.1 471 GAGAVMALCDDLYLQKAIEMAKKIQTIDLAGNVEFQKKFVYNLSFPE 517 ********************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (520 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.61 // [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