Align candidate WP_011033020.1 MM_RS05580 (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.21320.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-68 216.0 5.4 3.1e-67 212.5 5.5 2.2 2 lcl|NCBI__GCF_000007065.1:WP_011033020.1 MM_RS05580 DUF4445 domain-contai Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_011033020.1 MM_RS05580 DUF4445 domain-containing protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.6 0.0 0.013 0.013 142 172 .. 56 86 .. 53 89 .. 0.86 2 ! 212.5 5.5 3.1e-67 3.1e-67 1 260 [. 169 428 .. 169 429 .. 0.93 Alignments for each domain: == domain 1 score: 0.6 bits; conditional E-value: 0.013 RACo_C_ter 142 rakaAiyagvktLleevglevedidkvylaG 172 +a + ++vk +l+e+g++ e+++++ + G lcl|NCBI__GCF_000007065.1:WP_011033020.1 56 KAHGLSATAVKNILNELGVKPEEMERFAICG 86 566667789999***************9998 PP == domain 2 score: 212.5 bits; conditional E-value: 3.1e-67 RACo_C_ter 1 eislliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvigne 69 ei++ +D+GTNaE++l+++ ++++saaaGPAlEG+ei++G A+p++i +ve++ ++ +++ v++++ lcl|NCBI__GCF_000007065.1:WP_011033020.1 169 EIAIATDYGTNAEMALKSNGIIYTGSAAAGPALEGQEIEYGSIASPHTICDVEFEGNN--LRCYVLDRD 235 68899***************************************************99..555555543 PP RACo_C_ter 70 k......................pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteey 116 +kGi+G+G+i+li++ +++++i k+ +t+e lcl|NCBI__GCF_000007065.1:WP_011033020.1 236 MktakgdlinpktgevvekgevtAKGITGTGVIALIEAGMRNKLIVLP-KI-------------QTPEG 290 33466666899999999999999**********************664.66.............68999 PP RACo_C_ter 117 vlvlaeesetekdivitekDidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAit 185 vl+l++ i +t++D+ e+ ra++A++ag+ tL+ ++g+e+ed++ ++Ga G+y+d++kA++ lcl|NCBI__GCF_000007065.1:WP_011033020.1 291 VLYLQD------GIKFTNNDLIEAGRAIGALRAGHITLCAAAGIEMEDLKIAHMSGAAGTYMDAAKAHQ 353 **9997......8******************************************************** PP RACo_C_ter 186 iGllPdlelekvkqvGNtslagAraallsreareeleeiarki..tyielavekkFmeefvaalflpht 252 +G++P +++ v+q+GNtsl++Ar++lls+++++el++ia++i t++++a++++F+e ++ +l+++++ lcl|NCBI__GCF_000007065.1:WP_011033020.1 354 VGMIPY-NANYVSQIGNTSLTVAREILLSEDRLWELQTIAKQIlgTHVMFATSEAFKEAYLLELAYWNE 421 ******.************************************************************** PP RACo_C_ter 253 dlelfpsv 260 ++ +f+++ lcl|NCBI__GCF_000007065.1:WP_011033020.1 422 GM-AFKML 428 *9.68775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (261 nodes) Target sequences: 1 (539 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 4.53 // [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