Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate PP_1017 PP_1017 mannose/glucose ABC transporter, permease protein
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__Putida:PP_1017 Length = 281 Score = 126 bits (316), Expect = 6e-34 Identities = 86/271 (31%), Positives = 137/271 (50%), Gaps = 14/271 (5%) Query: 24 ILAILVVLTLGPIVFMVLTSLMDHNAIARGK---WIAPTRFSNYVEVFQKLPFGIYFRNS 80 +L I V+L L P+V M+LTS I G W A +V+ + + YF NS Sbjct: 20 VLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWPAVITGIGWVKAWGAVSG--YFWNS 77 Query: 81 LIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVKIK 140 +++ ++++ I L GY L+ ++F GS F L+L LP LLP K+ Sbjct: 78 IMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKLG 137 Query: 141 QATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLRVM 200 L ++ GLV+V+ + + F+ R F+ SIP L +AAR+DG FT F R++ Sbjct: 138 ------LASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRRII 191 Query: 201 LPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTA--RYDLLMA 258 LP++ P I+ I+ F W++ +F V+ I + + +T Y++ MA Sbjct: 192 LPMSTPIIMVCLIWQFTQIWNDFLFG-VVFSSGDSQPITVALNNLVNTSTGAKEYNVDMA 250 Query: 259 AGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289 A I +P L+++ K F+ G+TAGAVKG Sbjct: 251 AAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281 Lambda K H 0.332 0.145 0.434 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: 257 Number of extensions: 17 Number of successful extensions: 4 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: 289 Length of database: 281 Length adjustment: 26 Effective length of query: 263 Effective length of database: 255 Effective search space: 67065 Effective search space used: 67065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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