Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_045585061.1 AL072_RS29560 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_001305595.1:WP_045585061.1 Length = 301 Score = 379 bits (974), Expect = e-110 Identities = 194/303 (64%), Positives = 243/303 (80%), Gaps = 5/303 (1%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M+YF+QQL+NGL+LG+IYGL+AIGYTMVYGIIGMINFAHG+I+M+G F ALI FL + ++ Sbjct: 1 MDYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGAL 60 Query: 61 -FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFI 119 +P+A LL+MLV +ML TS++ WT+ER+AYRPLR S RLAPLI+AIGMSI L N+I Sbjct: 61 GITWVPLA--LLIMLVASMLFTSVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYI 118 Query: 120 QVTQGPRNKPIPPMVSS--VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQR 177 Q+ QG R+KP+ P++ G +SVS ++ IVIT VL+ F ++NRT+LGRAQR Sbjct: 119 QILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITLVLMVGFTILINRTSLGRAQR 178 Query: 178 ATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTA 237 A EQD+KMA LLGVNVD+ IS+TFVMGAALAAVAG M L+ YGV F GF GVK+FTA Sbjct: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKSFTA 238 Query: 238 AVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEV 297 AVLGG+GSLPGA+ GG++IGLIE+ WS Y +KDVATF+IL VLIF+PTG+LGRPE+ Sbjct: 239 AVLGGVGSLPGAMLGGVVIGLIEAFWSGYVGSEWKDVATFSILVLVLIFRPTGLLGRPEI 298 Query: 298 EKV 300 EKV Sbjct: 299 EKV 301 Lambda K H 0.329 0.143 0.421 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: 418 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: 300 Length of database: 301 Length adjustment: 27 Effective length of query: 273 Effective length of database: 274 Effective search space: 74802 Effective search space used: 74802 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