Align putative hydrolase, required for lysine catabolism (characterized)
to candidate AO353_21295 AO353_21295 hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_01105 (458 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21295 Length = 465 Score = 727 bits (1877), Expect = 0.0 Identities = 372/455 (81%), Positives = 403/455 (88%) Query: 4 VSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVLSEQPQLAEHLRSTGELERLD 63 VSPDLIRQRFSRAMSDMYR+EVPLYGALM+LV TN QVL P +A LRSTGE+ERLD Sbjct: 7 VSPDLIRQRFSRAMSDMYREEVPLYGALMELVAQTNVQVLDSDPAIARQLRSTGEIERLD 66 Query: 64 LERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQVSPF 123 LERHGAIRVGTA ELATL RLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHE++LQVSPF Sbjct: 67 LERHGAIRVGTAQELATLCRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHEASLQVSPF 126 Query: 124 RVFTSLLRLELIENSELRAFAESVLAKRQIFTPGALALIDLAERQGGLTQAQAEDFVLQA 183 RVFTSLLRLELIEN ELRAFAESVLAKR IFT AL LI+ AE+ GGL + QAEDFV QA Sbjct: 127 RVFTSLLRLELIENPELRAFAESVLAKRSIFTAQALKLIEQAEQHGGLDEQQAEDFVEQA 186 Query: 184 LETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPVHGI 243 LETFRWHH ATVTA QY+QLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQA+MP +GI Sbjct: 187 LETFRWHHRATVTAAQYQQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQAKMPEYGI 246 Query: 244 TPKAVIEGPPRRQCPILLRQTSFKALDEPVAFTDQPQAQGSHSARFGEIEQRGAALTPKG 303 TPKAVIEGPPRRQCPILLRQTSFKALDEP+AFTDQ QA GSHSARFGEIEQRGAALTP+G Sbjct: 247 TPKAVIEGPPRRQCPILLRQTSFKALDEPIAFTDQQQALGSHSARFGEIEQRGAALTPEG 306 Query: 304 RALYDQLLNAARDALGAFPNEANAERYNALMTEHFVAFPDNHDELRQQALAYFRYFPTPK 363 RALYD+LLNAARDAL FPNEANA RY++LM +HF AFPD+++E+R+Q LAYFRYF T K Sbjct: 307 RALYDRLLNAARDALNDFPNEANAARYHSLMEQHFKAFPDSYNEMREQGLAYFRYFVTEK 366 Query: 364 GLAAKGTLEPAASLEHLLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQSNR 423 GLAA +ASL LL+ +Y+RA PLVYEDFLPVSAAGIFQSNLGDAAQ+HY SNR Sbjct: 367 GLAADSDELGSASLRGLLDAEYIRAVPLVYEDFLPVSAAGIFQSNLGDAAQTHYGEHSNR 426 Query: 424 QAFEAALGRATIDELGLYAQTQQRSIDECRAALGV 458 QAFE ALGR+TIDEL LYA TQ+RSI+EC AAL V Sbjct: 427 QAFEQALGRSTIDELALYADTQRRSIEECCAALNV 461 Lambda K H 0.320 0.134 0.383 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: 778 Number of extensions: 18 Number of successful extensions: 1 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: 458 Length of database: 465 Length adjustment: 33 Effective length of query: 425 Effective length of database: 432 Effective search space: 183600 Effective search space used: 183600 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: 51 (24.3 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