Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_012172788.1 AZC_RS21905 histidinol-phosphatase
Query= reanno::Phaeo:GFF2154 (250 letters) >NCBI__GCF_000010525.1:WP_012172788.1 Length = 262 Score = 227 bits (579), Expect = 2e-64 Identities = 120/245 (48%), Positives = 154/245 (62%), Gaps = 2/245 (0%) Query: 1 MADAARQAILPYFRSA-GLQSDNKLD-EGFDPVTIADRAAEQAMRSVLSELRPEDSILGE 58 +A + +AILP+FR+A G++ + + FDPVT ADRAAEQ MR +++ PE I+GE Sbjct: 13 LATRSGEAILPFFRTAIGVEDKGRRKGQSFDPVTEADRAAEQVMRRMITTTFPEHGIIGE 72 Query: 59 EFGETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGT 118 EFG + W LDPIDGT+ FISG P WG LI L P G++ QP+IGERF G Sbjct: 73 EFGNERRDADYVWALDPIDGTKSFISGMPAWGTLIGLLKQGAPVYGMMHQPFIGERFFGD 132 Query: 119 PEGASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDC 178 A GP G L+TR L +A LFTT P + A+R FQ V VRL+RYG DC Sbjct: 133 GGSAHYLGPAGKRRLLTRDCGRLEDAILFTTSPLLMNAADRTLFQSVERDVRLSRYGGDC 192 Query: 179 YAYALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAEL 238 YAY ++AAG DLVIE GL +DI A + VI+ AGG+VTNW+G GG+V+AA + + Sbjct: 193 YAYCMVAAGLVDLVIETGLQDHDIVALVPVIEGAGGIVTNWEGGSPVAGGRVVAAGSKAV 252 Query: 239 HAAAL 243 H AL Sbjct: 253 HEQAL 257 Lambda K H 0.317 0.134 0.392 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: 219 Number of extensions: 12 Number of successful extensions: 2 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: 250 Length of database: 262 Length adjustment: 24 Effective length of query: 226 Effective length of database: 238 Effective search space: 53788 Effective search space used: 53788 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_012172788.1 AZC_RS21905 (histidinol-phosphatase)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))
# 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/TIGR02067.hmm # target sequence database: /tmp/gapView.667959.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02067 [M=252] Accession: TIGR02067 Description: his_9_HisN: histidinol-phosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-99 318.7 0.0 1.6e-99 318.5 0.0 1.0 1 NCBI__GCF_000010525.1:WP_012172788.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012172788.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.5 0.0 1.6e-99 1.6e-99 2 252 .] 7 261 .. 6 261 .. 0.98 Alignments for each domain: == domain 1 score: 318.5 bits; conditional E-value: 1.6e-99 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdk....tpVteADraaEeaireliaakfPddgilGEEfgeeee 70 +a++++la+ +geail++fr+ ++dk ++k +pVteADraaE+++r++i+++fP++gi+GEEfg+e+ NCBI__GCF_000010525.1:WP_012172788.1 7 DAFVHDLATRSGEAILPFFRTAIGVEDKGRRKgqsfDPVTEADRAAEQVMRRMITTTFPEHGIIGEEFGNERR 79 5899*****************99999999998999************************************** PP TIGR02067 71 daeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerelrvsev 142 da+yvW lDPiDGTksFi+G+P wgtLi+Ll++g+pv G+++qP++gerf+++ g++ +l + g+r+l ++ + NCBI__GCF_000010525.1:WP_012172788.1 80 DADYVWALDPIDGTKSFISGMPAWGTLIGLLKQGAPVYGMMHQPFIGERFFGDGGSAHYLGPaGKRRLLTRDC 152 ************************************************************98667******** PP TIGR02067 143 aklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiie 215 +l+dA+l+ttsp l++ ++r f++++r++rl+ryggdcyay++vA+G vdlv+e++l+ +Di al+p+ie NCBI__GCF_000010525.1:WP_012172788.1 153 GRLEDAILFTTSP-LLMNAADRTLFQSVERDVRLSRYGGDCYAYCMVAAGLVDLVIETGLQDHDIVALVPVIE 224 *************.8********************************************************** PP TIGR02067 216 eAggvitdwkGkeaeeggeavaaanaalhdevlellk 252 +Agg++t+w+G + +gg++vaa+++a+h+++l++l+ NCBI__GCF_000010525.1:WP_012172788.1 225 GAGGIVTNWEGGSPVAGGRVVAAGSKAVHEQALKRLN 261 *********************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (262 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: 14.73 // [ok]
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