Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_552 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_552 Length = 384 Score = 513 bits (1322), Expect = e-150 Identities = 247/371 (66%), Positives = 294/371 (79%), Gaps = 1/371 (0%) Query: 6 KLTVVAAIAAAAGVASAQE-QVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTI 64 +++ + A+A AA VASAQ+ Q VKI H PVSG AH GKD ENG R+AI++LNAQ + I Sbjct: 13 RISALTAVALAASVASAQDVQTVKIAHAGPVSGGIAHIGKDTENGVRLAIDDLNAQNLVI 72 Query: 65 GGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124 GGKKIKFE+ AEDDA DP+Q TA AQKLCD KVAGVVGHL SGT+IPAS +Y C +PH+ Sbjct: 73 GGKKIKFEIAAEDDAGDPRQATAVAQKLCDQKVAGVVGHLQSGTSIPASAIYAKCDLPHI 132 Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184 T +A+NP+LTKPG+KTTFR+IANDNALGA LA + D KLK+VAIIDDRTAYGQGVA V Sbjct: 133 TASASNPDLTKPGHKTTFRLIANDNALGAALALFGADHQKLKSVAIIDDRTAYGQGVASV 192 Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244 FK TA KG+KVV E+FT DKATDFMAILTAIK K PDAIFYGG+D Q GPMLRQMEQLG Sbjct: 193 FKATAQQKGLKVVAEEFTNDKATDFMAILTAIKNKKPDAIFYGGLDAQAGPMLRQMEQLG 252 Query: 245 MGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304 +GNVKYFGGD +CT ++ +L+ L NV CA GG+S+ KM GG WK +YDAK+P QF Sbjct: 253 LGNVKYFGGDALCTEKLPELSGKTPALKNVTCATGGASVDKMQGGADWKKRYDAKFPGQF 312 Query: 305 QVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITL 364 Q+YSPY YDA ++ DAMKRANSVDPKV+ P LAK+ +KGVT+ IAF GE+ PA+TL Sbjct: 313 QIYSPYAYDAAMVLADAMKRANSVDPKVFAPFLAKTEYKGVTANIAFTAKGELTTPAVTL 372 Query: 365 YVYKDGKKTPL 375 Y +KDG + L Sbjct: 373 YTFKDGSRVAL 383 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: 511 Number of extensions: 15 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: 375 Length of database: 384 Length adjustment: 30 Effective length of query: 345 Effective length of database: 354 Effective search space: 122130 Effective search space used: 122130 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