Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate SMc03133 SMc03133 amino-acid transport system permease ABC transporter protein
Query= TCDB::Q88NY4 (223 letters) >FitnessBrowser__Smeli:SMc03133 Length = 323 Score = 118 bits (295), Expect = 2e-31 Identities = 71/204 (34%), Positives = 116/204 (56%), Gaps = 7/204 (3%) Query: 17 EGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVITWFYL 76 +G+V TL + V+ + V+ + A+ +LS + ++ LA Y + FR +PLL+ I YL Sbjct: 120 QGVVTTLYISVISIAVATVIALVGAIAKLSKNGVIYGLATFYTSLFRGLPLLMQIYIIYL 179 Query: 77 AVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQALGMNY 136 +P V I+ P G ++A + AY EI RAG++SI +GQ A ALG++ Sbjct: 180 GLPQVGYVISA--VPAG-----ILALSLCYGAYMTEIFRAGIESIPRGQTEGATALGLSP 232 Query: 137 AQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARSNGDIIGRSHEFL 196 +QTM L+ILPQA R + P Q I + +D+SL+ VG+ + + AR+ G R E L Sbjct: 233 SQTMGLVILPQAMRVIIPPTGNQFIAMLKDSSLISVVGVWELMYLARTQGQTEFRHIEML 292 Query: 197 IFAGVVYFLISFSASWLVKRLQKR 220 I A ++Y+++S ++ R++ R Sbjct: 293 ITASMIYWILSIGLEYMQSRVEAR 316 Lambda K H 0.330 0.141 0.417 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: 195 Number of extensions: 12 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: 223 Length of database: 323 Length adjustment: 25 Effective length of query: 198 Effective length of database: 298 Effective search space: 59004 Effective search space used: 59004 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 (21.9 bits) S2: 47 (22.7 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