Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate 3606958 Dshi_0386 N-formylglutamate amidohydrolase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2548 (270 letters) >FitnessBrowser__Dino:3606958 Length = 287 Score = 85.1 bits (209), Expect = 2e-21 Identities = 76/242 (31%), Positives = 107/242 (44%), Gaps = 25/242 (10%) Query: 14 TAPLLVSMPHAG-TYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDMGASILVATHSRY 72 T ++ + PH+G Y L + D D ++ L A A GA + AT R Sbjct: 15 TTSVIFASPHSGRAYSKDFLRSTVLDTQTIRSSEDAFVDELIACAPRYGAQTIAATAPRA 74 Query: 73 VVDLNRPPDGASLYPG--------------QSVTGLCPVDTFDDTPIYAQGDVPDDAEVA 118 +DLNR D L P S G+ P + IY +G + + E Sbjct: 75 YIDLNRNAD--ELDPAVVSGLRRVTHNPRISSGLGVVPRVVANGRAIY-RGKMHLN-EAK 130 Query: 119 ARRDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIR----SVLPRFFEGKLPDLNLGTA 174 AR DA W PYH QLR L R G A+L D HS+ L + E + PD+ LG Sbjct: 131 ARLDAYWHPYHDQLRRMLDVTRNAFGQAILVDCHSMPHEAIDALHQHSEAR-PDVVLGDR 189 Query: 175 DGASCDPALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYM 234 GA+ + + A ++A G N F G I +HYG+P++N H VQ+E+ + YM Sbjct: 190 FGAASAAHIVDQVEAAFKNA-GLRVARNAPFAGAFIAQHYGRPSRNQHVVQIEIDRALYM 248 Query: 235 QE 236 E Sbjct: 249 DE 250 Lambda K H 0.321 0.135 0.416 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: 175 Number of extensions: 13 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: 270 Length of database: 287 Length adjustment: 25 Effective length of query: 245 Effective length of database: 262 Effective search space: 64190 Effective search space used: 64190 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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