Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS17350 HSERO_RS17350 ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS17350 Length = 380 Score = 415 bits (1067), Expect = e-121 Identities = 216/377 (57%), Positives = 264/377 (70%), Gaps = 5/377 (1%) Query: 3 LKLKLTVV---AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNA 59 +KLK ++ AAI A A+ ++VVKI HV P+SG AH GKDNENGARMA++ELNA Sbjct: 1 MKLKSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNA 60 Query: 60 QGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDC 119 +G TIGGKK+KFELV EDDA+DPKQ TA A KL D KVA V+GHLNSGTTIPASK+Y+D Sbjct: 61 KGFTIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDA 120 Query: 120 GIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQ 179 GIP V+ +ATNP T+ G+KT FR++AND LGA L YAV L K +A+IDDRTAYGQ Sbjct: 121 GIPQVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQ 180 Query: 180 GVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQ 239 GVAD F K A A G +V Q+T DKATDF AILT++K K PD +F+GGMD GGPMLRQ Sbjct: 181 GVADEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQ 240 Query: 240 MEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAE-GGSSLAKMPGGTAWKAKYDA 298 M+QLG+ + K+ GGDGICT + LA VICAE GG A G ++A Y Sbjct: 241 MKQLGI-SAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKK 299 Query: 299 KYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMK 358 K+ + Y YDAT + DAM +A S DPK Y PELAK S KGVT IAF+ G++K Sbjct: 300 KFGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIK 359 Query: 359 NPAITLYVYKDGKKTPL 375 + ++TLY YK G++T L Sbjct: 360 DGSLTLYTYKGGQRTLL 376 Lambda K H 0.315 0.131 0.375 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: 539 Number of extensions: 17 Number of successful extensions: 3 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: 375 Length of database: 380 Length adjustment: 30 Effective length of query: 345 Effective length of database: 350 Effective search space: 120750 Effective search space used: 120750 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: 42 (22.0 bits) S2: 50 (23.9 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