Align putative hydrolase, required for lysine catabolism (characterized)
to candidate Pf6N2E2_134 FIG00960493: hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_01105 (458 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_134 Length = 458 Score = 833 bits (2153), Expect = 0.0 Identities = 424/458 (92%), Positives = 439/458 (95%) Query: 1 MSFVSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVLSEQPQLAEHLRSTGELE 60 MSFVSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVL+E P LA HLRSTGELE Sbjct: 1 MSFVSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVLAEDPILAAHLRSTGELE 60 Query: 61 RLDLERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQV 120 RLDLERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQV Sbjct: 61 RLDLERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQV 120 Query: 121 SPFRVFTSLLRLELIENSELRAFAESVLAKRQIFTPGALALIDLAERQGGLTQAQAEDFV 180 SPFRVFTSLLRLELIE++ELRAFAESVL KRQIFTP AL LI+ AE QGGL+++QAEDFV Sbjct: 121 SPFRVFTSLLRLELIEHAELRAFAESVLDKRQIFTPRALELIEQAEYQGGLSESQAEDFV 180 Query: 181 LQALETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPV 240 LQALETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPV Sbjct: 181 LQALETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPV 240 Query: 241 HGITPKAVIEGPPRRQCPILLRQTSFKALDEPVAFTDQPQAQGSHSARFGEIEQRGAALT 300 HGITPKAVIEGPPRRQCPILLRQTSFKALDEPV+FTDQ +QGSHSARFGEIEQRGAALT Sbjct: 241 HGITPKAVIEGPPRRQCPILLRQTSFKALDEPVSFTDQSPSQGSHSARFGEIEQRGAALT 300 Query: 301 PKGRALYDQLLNAARDALGAFPNEANAERYNALMTEHFVAFPDNHDELRQQALAYFRYFP 360 PKGRALYD+LLNAARDALG FPNEANAERYN LM+EHF FPDNHDELR++ALAYFRYF Sbjct: 301 PKGRALYDRLLNAARDALGDFPNEANAERYNTLMSEHFAQFPDNHDELRREALAYFRYFV 360 Query: 361 TPKGLAAKGTLEPAASLEHLLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQ 420 TPKGLAAKG++E ASLE LLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQ Sbjct: 361 TPKGLAAKGSVERTASLERLLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQ 420 Query: 421 SNRQAFEAALGRATIDELGLYAQTQQRSIDECRAALGV 458 SNR AFEAALGRATIDELGLYAQTQQRSIDECRAALGV Sbjct: 421 SNRHAFEAALGRATIDELGLYAQTQQRSIDECRAALGV 458 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: 876 Number of extensions: 22 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: 458 Length adjustment: 33 Effective length of query: 425 Effective length of database: 425 Effective search space: 180625 Effective search space used: 180625 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