Align candidate WP_011306071.1 MBAR_RS05670 (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.28252.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-68 214.2 7.9 1.3e-67 213.7 6.3 2.0 2 lcl|NCBI__GCF_000195895.1:WP_011306071.1 MBAR_RS05670 DUF4445 domain-cont Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_011306071.1 MBAR_RS05670 DUF4445 domain-containing protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.0 0.053 0.053 142 172 .. 56 86 .. 53 88 .. 0.85 2 ! 213.7 6.3 1.3e-67 1.3e-67 2 260 .. 170 428 .. 169 429 .. 0.95 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.053 RACo_C_ter 142 rakaAiyagvktLleevglevedidkvylaG 172 +a + ++vk +l e+g+++ +++k+ + G lcl|NCBI__GCF_000195895.1:WP_011306071.1 56 KAHGLSATAVKNILAELGVNLAEMEKFSICG 86 5666667899999**************9998 PP == domain 2 score: 213.7 bits; conditional E-value: 1.3e-67 RACo_C_ter 2 islliDiGTNaEivlgnkdwllaasaaaGPAlEGgeikcGmrAapgAierveidpetlevelkvignek 70 +++ +D+GTNaE++l+ + +++++saaaGPAlEG+ei++G A+p++i++ve++ e+ +++ v++++ lcl|NCBI__GCF_000195895.1:WP_011306071.1 170 VAIATDYGTNAEMALKANGVIYTGSAAAGPALEGQEIEYGSIASPHTISDVEFEGEN--LRCYVLDKDM 236 6799***************************************************99..7777777655 PP RACo_C_ter 71 ......................pkGicGsGiidliaelleagiidkkgklnkelkserireeeeteeyv 117 +kGi+G+G+i+li++ +++++i k+ +t++ v lcl|NCBI__GCF_000195895.1:WP_011306071.1 237 tatkgdlvnpktgeivekeeltAKGITGTGVIALIEAGMRNKLIVLP-KI-------------QTPDGV 291 667788899999********************************664.66.............68999* PP RACo_C_ter 118 lvlaeesetekdivitekDidelirakaAiyagvktLleevglevedidkvylaGafGsyidlekAiti 186 ++l++ i +t+kD+ e+ ra++Ai+ag+ tL+ ++g+++e++++ ++Ga G+y+d++kA+++ lcl|NCBI__GCF_000195895.1:WP_011306071.1 292 IHLQD------GIKFTNKDLIEAGRAIGAIRAGHITLCAAAGIDMEELQTAHMSGAAGTYMDAAKAHKV 354 **997......8********************************************************* PP RACo_C_ter 187 GllPdlelekvkqvGNtslagAraallsreareeleeiarki..tyielavekkFmeefvaalflphtd 253 G++P +++ v+q+GNtsl++Ar++lls+++++el++ia++i t++++a++++F+e ++ +l++++++ lcl|NCBI__GCF_000195895.1:WP_011306071.1 355 GMIPY-NANYVSQIGNTSLTVAREILLSEDRLWELQAIAKEIvgTHVMFATSDAFKEAYMLELAYWNEG 422 *****.*************************************************************** PP RACo_C_ter 254 lelfpsv 260 + +f+++ lcl|NCBI__GCF_000195895.1:WP_011306071.1 423 M-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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 3.46 // [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