Align putative hydrolase, required for lysine catabolism (characterized)
to candidate Pf1N1B4_5865 FIG00960493: hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_01105 (458 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5865 Length = 463 Score = 735 bits (1898), Expect = 0.0 Identities = 371/457 (81%), Positives = 406/457 (88%), Gaps = 2/457 (0%) Query: 2 SFVSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVLSEQPQLAEHLRSTGELER 61 +F+SPDLIRQRFS+AMSDMYR+EVPLYGALM+LVE TN VL PQ+A L STGE++R Sbjct: 5 NFISPDLIRQRFSKAMSDMYREEVPLYGALMELVEQTNRHVLDSDPQIARQLHSTGEIQR 64 Query: 62 LDLERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQVS 121 LDLERHGAIRVGTAAEL+TL RLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHE+ALQVS Sbjct: 65 LDLERHGAIRVGTAAELSTLARLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHEAALQVS 124 Query: 122 PFRVFTSLLRLELIENSELRAFAESVLAKRQIFTPGALALIDLAERQGGLTQAQAEDFVL 181 PFRVFTSLLRLELIE++ELRAFA+SVL R IFTP ALALI+ AE QGGLT+ +A+DFV Sbjct: 125 PFRVFTSLLRLELIEDAELRAFAQSVLDTRSIFTPAALALIERAETQGGLTEYEAQDFVA 184 Query: 182 QALETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPVH 241 QALETFRWHHSATVTAEQY+QLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQA+MP H Sbjct: 185 QALETFRWHHSATVTAEQYQQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQAQMPAH 244 Query: 242 GITPKAVIEGPPRRQCPILLRQTSFKALDEPVAFTDQPQAQGSHSARFGEIEQRGAALTP 301 GITPKAVIEGPPRRQCPILLRQTSFKALDEP+ FTDQ Q +GSHSARFGEIEQRGAALTP Sbjct: 245 GITPKAVIEGPPRRQCPILLRQTSFKALDEPITFTDQAQTRGSHSARFGEIEQRGAALTP 304 Query: 302 KGRALYDQLLNAARDALGAFPNEANAERYNALMTEHFVAFPDNHDELRQQALAYFRYFPT 361 KGRALYD+LLNAARD L FPNEANA RYNALMT+HF FPD +++RQQ LA+FRYF T Sbjct: 305 KGRALYDRLLNAARDELKDFPNEANAARYNALMTQHFGEFPDTVEDMRQQELAFFRYFVT 364 Query: 362 PKGLAAKGTLEPAASLEHLLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQS 421 KGLAAKG SLE LL Y+R EPLVYEDFLPVSAAGIFQSNLGDAAQ+HY S Sbjct: 365 EKGLAAKGL--NGVSLEDLLRDGYVRVEPLVYEDFLPVSAAGIFQSNLGDAAQTHYGVHS 422 Query: 422 NRQAFEAALGRATIDELGLYAQTQQRSIDECRAALGV 458 N+QAFE ALGR+TIDELGLYA+TQ+RS+DEC LG+ Sbjct: 423 NQQAFEKALGRSTIDELGLYAETQRRSVDECCKTLGL 459 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: 792 Number of extensions: 23 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: 458 Length of database: 463 Length adjustment: 33 Effective length of query: 425 Effective length of database: 430 Effective search space: 182750 Effective search space used: 182750 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