Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_012171466.1 AZC_RS15205 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000010525.1:WP_012171466.1 Length = 305 Score = 391 bits (1004), Expect = e-113 Identities = 195/305 (63%), Positives = 247/305 (80%), Gaps = 4/305 (1%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGS- 59 M+ FLQQLINGL+LG+IYGLIAIGYTMV+GIIGM+NFAHG+++M+ +F+ LI FL + + Sbjct: 1 MDVFLQQLINGLTLGSIYGLIAIGYTMVFGIIGMVNFAHGDVFMVSSFIGLIAFLLLTTV 60 Query: 60 LGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119 LGI+ + L L ++LV +MLFT + WT+ER+AYRPLR S RLAP+ISAIGMSI L N+VQ Sbjct: 61 LGISSIFLVLAIVLVVAMLFTGLLSWTIERVAYRPLRGSFRLAPMISAIGMSILLANFVQ 120 Query: 120 ILQGARSKPLQPILPGNLTLMDG---AVSVSYVRLATIVITIALMYGFTQLITRTSLGRA 176 + QG R+KPL PI+P + LMD V+++Y ++ + +T+AL+ GF L+ +T LGRA Sbjct: 121 VAQGPRNKPLPPIIPDVIVLMDNNGYQVTLAYKQIVIMAVTVALLAGFWYLVQKTPLGRA 180 Query: 177 QRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAF 236 QRACEQD+KMA LLGV+VDR ISLTFV+GA LAAVAG M L+ YGV++F GF+ GVKAF Sbjct: 181 QRACEQDRKMAALLGVDVDRTISLTFVIGAMLAAVAGTMYLMYYGVVNFNDGFVPGVKAF 240 Query: 237 TAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRP 296 TAAVLGGIGSLPGA+LGG++IGLIE FWS Y E+KDVA F+IL + LIF P GLLGRP Sbjct: 241 TAAVLGGIGSLPGAVLGGLLIGLIETFWSAYFSIEYKDVAAFSILAITLIFMPQGLLGRP 300 Query: 297 EIEKV 301 E+EKV Sbjct: 301 EVEKV 305 Lambda K H 0.329 0.144 0.425 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: 406 Number of extensions: 11 Number of successful extensions: 4 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: 301 Length of database: 305 Length adjustment: 27 Effective length of query: 274 Effective length of database: 278 Effective search space: 76172 Effective search space used: 76172 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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