Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate Echvi_2457 Echvi_2457 histidinol-phosphatase
Query= SwissProt::D2QPE6 (382 letters) >FitnessBrowser__Cola:Echvi_2457 Length = 365 Score = 520 bits (1338), Expect = e-152 Identities = 257/382 (67%), Positives = 294/382 (76%), Gaps = 17/382 (4%) Query: 1 MQKIVFIDRDGTLIAEPQPDQQVDSLAKLDFIPKAISAMRKIAEDTTYELVMVTNQDGLG 60 M+K++FIDRDGT+I EP D QVDSL KL+F PKAIS +RKIAE+T YELVMVTNQDGLG Sbjct: 1 MKKVLFIDRDGTIIKEPPVDYQVDSLEKLEFYPKAISNLRKIAEETDYELVMVTNQDGLG 60 Query: 61 TGSFPEDTFWPAHNKMMSTFAGENVNFAAVHIDRHFPHDNSSTRKPGVGMLTQYFEASYD 120 T SFPEDTFWPA KM+ T E V F+A+HID+ F H+N+ TRKP G+LT Y + YD Sbjct: 61 TDSFPEDTFWPAQYKMLKTLEEEGVVFSAIHIDKTFEHENAPTRKPRTGLLTDYLKGDYD 120 Query: 121 LTNSFVIGDRLTDVQLAVNLGAKAILFMPPNGLAAVQSADVSGLTEAMKQAIVLQTGDWD 180 L +SFVIGDR TDVQLA NLG +AI + E + L T WD Sbjct: 121 LAHSFVIGDRKTDVQLAKNLGTQAIF-----------------IGEEAAEGAALSTTSWD 163 Query: 181 EIYEFLRLPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADL 240 EIYEFLRLP+R V+R+T ETQI + +NLDG G+ + TGL FFDHML+Q+ KH G DL Sbjct: 164 EIYEFLRLPSRIGQVKRSTSETQIEIMVNLDGSGKCQIDTGLPFFDHMLEQLGKHGGTDL 223 Query: 241 AIHVNGDLHIDEHHTIEDTALALGEAYRRALGDKRGISRYGFLLPMDEALAQVGIDFSGR 300 I VNGDLHIDEHHTIEDTALALGEAY +ALGDK+GI RYGFLLPMD+ LAQV IDF GR Sbjct: 224 DIKVNGDLHIDEHHTIEDTALALGEAYLKALGDKKGIYRYGFLLPMDDVLAQVAIDFGGR 283 Query: 301 PWLVWDAEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIKVEGDNEHHKIEAIFKAFAKA 360 PW++W+AEF REKIGDMPTEMFYHFFKSFSDTA CNLNIK EG NEHHKIEAIFK A+A Sbjct: 284 PWMMWEAEFNREKIGDMPTEMFYHFFKSFSDTAKCNLNIKAEGANEHHKIEAIFKGLARA 343 Query: 361 IKMAVRRDINELDNLPSTKGVL 382 IKMAV+RDI L+ LPSTKGVL Sbjct: 344 IKMAVKRDIAALNQLPSTKGVL 365 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: 472 Number of extensions: 22 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: 382 Length of database: 365 Length adjustment: 30 Effective length of query: 352 Effective length of database: 335 Effective search space: 117920 Effective search space used: 117920 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)
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