Align gamma-glutamyl-gamma-aminobutyrate hydrolase (EC: 3.5.1.94) (characterized)
to candidate Ac3H11_1167 Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85)
Query= reanno::SB2B:6936606 (267 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1167 Length = 296 Score = 112 bits (279), Expect = 1e-29 Identities = 85/241 (35%), Positives = 120/241 (49%), Gaps = 24/241 (9%) Query: 45 SDCIPLLIP-----TCFGVADIEQYLDMADGVYLSGAASNIDPSLYGQENLTPEKKQDLA 99 S I +++P T G ++ Y + DGV + G A ++ P YG+E L E D Sbjct: 44 SGAIVVMVPCPTGETARGDVTLQHYAEWLDGVVMHGGA-DVWPGNYGEEPLREEWVGDRV 102 Query: 100 RDLVDIALIKGAVKRGLPILGICRGMQEMNIAFGGDLYQKVHDEDHLNDHREDPDTPPDV 159 RD+ D+AL+K + G PI G+CRG+Q +N+AFGG LYQ + + H + T D Sbjct: 103 RDIYDLALVKAFAEVGKPIFGVCRGLQLINVAFGGALYQDI-ETQHPGALQHRNATTYDQ 161 Query: 160 QYGASHSISMVKGSWLHKLLGDT--IEVNSLHGQGIKTLGKGLEALALAE-DGLVEALHA 216 + H I +V S L KL D VNS+H QGIK + E AL+E DG+ EA+ Sbjct: 162 HF---HGIQIVPDSHLAKLYPDVPRARVNSIHHQGIKRVAPEFEVEALSEPDGVPEAIRL 218 Query: 217 PYLP--QFTLGVQWHPEW--KALENPDSIKIFKAFGEACRR------RAGSALDLRIDKA 266 P + QWHPE+ K + D I + F AC R G + LR D+A Sbjct: 219 KPAPGRGYIAATQWHPEFHKKGSDTLDDTAILQDFLAACAEARKNPVRPGQPVGLR-DRA 277 Query: 267 S 267 + Sbjct: 278 T 278 Lambda K H 0.318 0.137 0.412 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: 200 Number of extensions: 6 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: 267 Length of database: 296 Length adjustment: 26 Effective length of query: 241 Effective length of database: 270 Effective search space: 65070 Effective search space used: 65070 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)
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