Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= SwissProt::P22729 (425 letters) >MicrobesOnline__882:209488 Length = 407 Score = 323 bits (829), Expect = 5e-93 Identities = 165/314 (52%), Positives = 219/314 (69%), Gaps = 20/314 (6%) Query: 93 LVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYT 152 L+A+LV+ P +VS +I ++Y++LGLGLN+VVGLSG LVLGY FYA+GAY Sbjct: 93 LLAVLVVFAVLPMLVSTYQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYA 152 Query: 153 FALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNN 212 +ALLN +GLGFWT LPI G +AA G LLGFPVLRL+GDYLAIVTLGFGEIVR++L N Sbjct: 153 YALLNADFGLGFWTVLPIGGALAAVFGILLGFPVLRLKGDYLAIVTLGFGEIVRLVLENW 212 Query: 213 TEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLV 272 +T GP+GIS+I +P LFG+E S S+ ++Y + L V Sbjct: 213 GSVTRGPSGISKIARPGLFGMELS--------------------VSEATTYIYYLILAAV 252 Query: 273 VLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAA 332 + ++F + RL +GRAW+ALREDEIAC ++G+ KLTAF + A +AGFAG +FAA Sbjct: 253 IFTIFAVGRLKDSRIGRAWQALREDEIACEAMGIDLTTTKLTAFALGACWAGFAGVIFAA 312 Query: 333 RQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGG 392 + F++P SFTF ESA +LA+VVLGGMGS V+L A++L++ E +R F+EY ML+ G Sbjct: 313 KTTFINPASFTFLESAMILAMVVLGGMGSTLGVVLGALVLILLPEYLRAFSEYRMLIFGA 372 Query: 393 LMVLMMIWRPQGLL 406 MVLMM++RPQGL+ Sbjct: 373 AMVLMMVFRPQGLV 386 Lambda K H 0.330 0.145 0.436 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: 390 Number of extensions: 10 Number of successful extensions: 2 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: 425 Length of database: 407 Length adjustment: 31 Effective length of query: 394 Effective length of database: 376 Effective search space: 148144 Effective search space used: 148144 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 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