Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate RR42_RS34790 RR42_RS34790 ABC transporter permease
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS34790 Length = 348 Score = 161 bits (408), Expect = 3e-44 Identities = 98/323 (30%), Positives = 169/323 (52%), Gaps = 25/323 (7%) Query: 86 TVKQKLFLVALLVLAVAWPFMVSRGT-VDIATLTMIYIILGLGLNVVVGLSGLLVLGYGG 144 T++ K LL LA+A+P + + + TL IY I LGLN++ G +G L L +GG Sbjct: 4 TLQGKTGWALLLALAIAFPLVTPNSYYLTVMTLAFIYAIATLGLNLITGYTGQLNLAHGG 63 Query: 145 FYAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEI 204 F AIGAYT +L + + FW ++G++ G+ +G LRL+G Y +I TL G I Sbjct: 64 FMAIGAYTLGILTVDHQVPFWAAFVLSGVVCMMVGYFVGVVSLRLKGHYFSIFTLCIGYI 123 Query: 205 VRILLLNNTEITGGPNGISQIPKPTLFG-LEFSRTAREGGWDTFSNFFGLKYDPSDRVIF 263 + +L+ +T G G+ IP P G L F D V Sbjct: 124 IYLLIEKWESLTHGTVGLIGIPVPASVGPLAF-----------------------DNVQA 160 Query: 264 LYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFA 323 Y + L +V F+++R++ LGR++ A+R + +LG++ R K+ +F +S +A Sbjct: 161 QYYLVLFFLVAGTFLMHRIVTSLLGRSFMAVRNSDALAEALGINLMRTKVLSFVLSVGYA 220 Query: 324 GFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFN 383 GFAG L+A + F+ P+ + ++ +++GG G+ +L A+L+ + ++ Sbjct: 221 GFAGALYAGQVRFLGPDIARTDLTFEMVMAMLVGGTGTLLGPLLGAVLVPWVTQTLQFLQ 280 Query: 384 EYSMLMLGGLMVLMMIWRPQGLL 406 +Y ML+ G ++VL++I+ P G++ Sbjct: 281 DYRMLVFGPVLVLLIIFVPDGIV 303 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: 251 Number of extensions: 10 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: 425 Length of database: 348 Length adjustment: 30 Effective length of query: 395 Effective length of database: 318 Effective search space: 125610 Effective search space used: 125610 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