Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate Ac3H11_2065 Maltose/maltodextrin ABC transporter, permease protein MalG
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2065 Length = 289 Score = 109 bits (272), Expect = 1e-28 Identities = 63/213 (29%), Positives = 108/213 (50%), Gaps = 1/213 (0%) Query: 173 GMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIP 232 G+ F N++ + +PA +I + A Y L+ +F G L +++ + +P Q+ L+P Sbjct: 77 GLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFGMLLFGVFMPFQVVLLP 136 Query: 233 LLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFT 292 + + +G+ G L H G+ RNY +P++++ A++DGA+ FQIF Sbjct: 137 MSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELVNAARMDGASFFQIFW 196 Query: 293 KIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEI 352 +IVLPLS P + I+QF WND L VF + TV N + + + + Sbjct: 197 RIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVFSGTDSKPVTVGLNNLANTSSSVKA-YNV 255 Query: 353 LATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 AA ++ ++++ +F VRGL AG+VK Sbjct: 256 DMAAAIIAGLPTMVIYVLAGKFFVRGLTAGAVK 288 Score = 23.9 bits (50), Expect = 0.006 Identities = 9/22 (40%), Positives = 16/22 (72%) Query: 26 WLLPTFGLFVSSFRTVEQISSS 47 +LLP + + V+SF+ E+I S+ Sbjct: 27 FLLPLYAMLVTSFKYAEEIRST 48 Lambda K H 0.323 0.138 0.419 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: 293 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 385 Length of database: 289 Length adjustment: 28 Effective length of query: 357 Effective length of database: 261 Effective search space: 93177 Effective search space used: 93177 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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