Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate CA265_RS03625 CA265_RS03625 bifunctional imidazole glycerol-phosphate dehydratase/histidinol phosphatase
Query= SwissProt::D2QPE6 (382 letters) >FitnessBrowser__Pedo557:CA265_RS03625 Length = 377 Score = 480 bits (1236), Expect = e-140 Identities = 237/382 (62%), Positives = 285/382 (74%), Gaps = 5/382 (1%) Query: 1 MQKIVFIDRDGTLIAEPQPDQQVDSLAKLDFIPKAISAMRKIAEDTTYELVMVTNQDGLG 60 M+K++FIDRDGTL EP D+QVDS AKL F P+++ + KIA + YELVMVTNQDGLG Sbjct: 1 MKKVLFIDRDGTLNIEPD-DEQVDSFAKLKFYPRSLYYLSKIAAELDYELVMVTNQDGLG 59 Query: 61 TGSFPEDTFWPAHNKMMSTFAGENVNFAAVHIDRHFPHDNSSTRKPGVGMLTQYFEASYD 120 T S PE+ FWP HN M+ TF GE V+F+ + IDR F DN+ TRKPG +LT+YF YD Sbjct: 60 TLSNPEENFWPIHNFMLDTFEGEGVHFSEIVIDRTFAKDNAPTRKPGTALLTKYFSEDYD 119 Query: 121 LTNSFVIGDRLTDVQLAVNLGAKAILFMPPNGLAAVQSADVSGLTEAMKQAIVLQTGDWD 180 L NSFVIGDRL DV LA NLGAKAI + L + ++ D E + I+L+T W+ Sbjct: 120 LKNSFVIGDRLNDVVLAKNLGAKAIFLRQNDALGSTEALDKH---ETLLDVIILETKKWE 176 Query: 181 EIYEFLRLPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADL 240 +IY L+ +R ER T ET I + L+LDG G+A + TGL FFDHMLDQ+A+H DL Sbjct: 177 DIYNLLKAGSRKIHHERKTNETDITINLDLDGTGKAKIETGLNFFDHMLDQIARHGSVDL 236 Query: 241 AIHVNGDLHIDEHHTIEDTALALGEAYRRALGDKRGISRYGFLLPMDEALAQVGIDFSGR 300 + GDLHIDEHHTIEDT +ALGEA+ + LG+K GI RYGF LPMD+ LAQV IDF GR Sbjct: 237 EVIAKGDLHIDEHHTIEDTGIALGEAFAKGLGNKLGIERYGFCLPMDDCLAQVAIDFGGR 296 Query: 301 PWLVWDAEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIKVEGDNEHHKIEAIFKAFAKA 360 W+VWDAEFKREK+GDMPTEMFYHFFKSFSD A CNLN+K EGDNEHHKIEAIFKAFAKA Sbjct: 297 NWIVWDAEFKREKVGDMPTEMFYHFFKSFSDAAKCNLNVKAEGDNEHHKIEAIFKAFAKA 356 Query: 361 IKMAVRRDINELDNLPSTKGVL 382 IKMA++RD ++ LPSTKG+L Sbjct: 357 IKMAIKRDAEKM-VLPSTKGLL 377 Lambda K H 0.320 0.136 0.403 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: 451 Number of extensions: 14 Number of successful extensions: 3 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: 382 Length of database: 377 Length adjustment: 30 Effective length of query: 352 Effective length of database: 347 Effective search space: 122144 Effective search space used: 122144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate CA265_RS03625 CA265_RS03625 (bifunctional imidazole glycerol-phosphate dehydratase/histidinol phosphatase)
to HMM TIGR01261 (hisB: 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/TIGR01261.hmm # target sequence database: /tmp/gapView.32261.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01261 [M=161] Accession: TIGR01261 Description: hisB_Nterm: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-50 156.0 0.0 4.7e-50 155.3 0.0 1.3 1 lcl|FitnessBrowser__Pedo557:CA265_RS03625 CA265_RS03625 bifunctional imida Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03625 CA265_RS03625 bifunctional imidazole glycerol-phosphate dehydratase/histid # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 155.3 0.0 4.7e-50 4.7e-50 1 149 [. 2 149 .. 2 158 .. 0.96 Alignments for each domain: == domain 1 score: 155.3 bits; conditional E-value: 4.7e-50 TIGR01261 1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklk.eagyklvlvtnqdGlGtesfPkedf 67 +k+lfidrdGtl eP d qvd++ klk+ + + l k+ e++y+lv+vtnqdGlGt s P+e+f lcl|FitnessBrowser__Pedo557:CA265_RS03625 2 KKVLFIDRDGTLNIEPD-DEQVDSFAKLKFYPRSLYYLSKIAaELDYELVMVTNQDGLGTLSNPEENF 68 589*************9.99********************96379*********************** PP TIGR01261 68 dkphalmlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlql 135 h++ml+ f+ eG++f++++i++ f +dn+ +rkP ++ll++y+ +e++d ++s+viGdr d+ l lcl|FitnessBrowser__Pedo557:CA265_RS03625 69 WPIHNFMLDTFEGEGVHFSEIVIDRTFAKDNAPTRKPGTALLTKYF-SEDYDLKNSFVIGDRLNDVVL 135 **********************************************.789****************** PP TIGR01261 136 aenlgirglkykee 149 a+nlg +++ ++++ lcl|FitnessBrowser__Pedo557:CA265_RS03625 136 AKNLGAKAIFLRQN 149 ********988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (377 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.15 // [ok]
This GapMind analysis is from Apr 09 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