Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_004327831.1 C665_RS19165 urea ABC transporter permease subunit UrtB
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000310185.1:WP_004327831.1 Length = 465 Score = 129 bits (323), Expect = 2e-34 Identities = 91/292 (31%), Positives = 147/292 (50%), Gaps = 16/292 (5%) Query: 8 LLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLPVA 67 L +GL+LGSI L A+G + YG++G+IN AHG++ M+G +A +V V + F + Sbjct: 172 LFSGLSLGSILLLAALGLAITYGVMGVINMAHGELLMVGAYATFLVQGVFRAHFPEY-LD 230 Query: 68 VLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQGPRN 127 +L + A L +L +ER+ R L G L L+ G+S+ L +V GP+N Sbjct: 231 FYVLAAIPAAFLAAALVGIAMERLVLRHLYGR-PLESLLATWGLSLVLIQAARVLFGPQN 289 Query: 128 KPIPP---MVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDRK 184 + M V G + + +I+I+ A +L + W ++ +T LG RA Q+R Sbjct: 290 LELANPSWMSGGVKLAGGVVLPYNRIVILGFAAFVLVLIWLMMQKTRLGMFVRAVTQNRP 349 Query: 185 MAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPG--VKAFTAAVLGG 242 MA +GV + ++ F +G+ +A + G L +A+ G V AF VLGG Sbjct: 350 MAGCVGVPTARVDTLAFAIGSGVAGLGG---LALSQIANVGPAMGTGYIVDAFMVVVLGG 406 Query: 243 IGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIF---KPTGI 291 +G L GAV+ L +G++ + A VA +L F++ F +P GI Sbjct: 407 VGQLAGAVWAALGLGIVAKFLEGW---AGAVVAKILVLVFIIAFIQKRPQGI 455 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: 313 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 300 Length of database: 465 Length adjustment: 30 Effective length of query: 270 Effective length of database: 435 Effective search space: 117450 Effective search space used: 117450 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: 50 (23.9 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