Align Fructose import permease protein FrcC (characterized)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 136 bits (343), Expect = 7e-37 Identities = 94/306 (30%), Positives = 153/306 (50%), Gaps = 20/306 (6%) Query: 56 VLSLIAFGV-----ILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110 V+ L A G+ +L F S M + ++ GI + + DLSVG+++ Sbjct: 26 VMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVI 85 Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170 + V+ R L V L +G + G ING ++A++++ I TL QIV Sbjct: 86 ACAGVVAA-VVMRDTNSVFLGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRG 144 Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNA-VFTYGVVVMVLLVCLLWY--VLNR 227 ++++ + + S F GN +F V +++ +VC L++ +LN Sbjct: 145 LAYIFANGKAVGVSQESF-----------FVFGNGQMFGVPVPILITIVCFLFFGWLLNY 193 Query: 228 TAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQF 287 T +GR A+G + EAA LAGVNV R I I+ + G+I ALAG L R+ S P GQ Sbjct: 194 TTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQG 253 Query: 288 ANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIII 347 + I+A V+GG+SL GG G I ++ G LI+ + + L D + Y++ G ++++ Sbjct: 254 FELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLL 313 Query: 348 AVAIDQ 353 AV ID+ Sbjct: 314 AVVIDR 319 Lambda K H 0.327 0.141 0.420 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: 316 Number of extensions: 14 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: 1 Length of query: 360 Length of database: 323 Length adjustment: 29 Effective length of query: 331 Effective length of database: 294 Effective search space: 97314 Effective search space used: 97314 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 (21.7 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