Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate H281DRAFT_02176 H281DRAFT_02176 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_02176 Length = 321 Score = 161 bits (407), Expect = 2e-44 Identities = 111/316 (35%), Positives = 167/316 (52%), Gaps = 22/316 (6%) Query: 2 IKRNLPLMIT-IGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGG 60 +K+NLP+++ + + VLG L ++ FAS I + N+ +I+VGM FVI++GG Sbjct: 1 MKKNLPILLALVALVVLG----LVRYEHFASAYNITSFWRYNSMFALISVGMAFVIITGG 56 Query: 61 IDLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIIT 120 IDLSVG+V A + V A G ++A G A G G++I LKI FI+T Sbjct: 57 IDLSVGTVAAMSSVVAALASAHGGWVAVVAG---CAAGLAVGVLNGVIITRLKILPFIVT 113 Query: 121 LAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAM---GLLMLAVVVIGI 177 LA GV+ L+ + S + G G L + G++ V V G Sbjct: 114 LATSLGAHGVALLLGKNDA------VSIASDSNFANFGQGDLFGLPIPGIVAALVAVAGW 167 Query: 178 FLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYA 237 TRFG AIGG+ +A LMG++ T + Y +S LA +AG++ + AG Sbjct: 168 LALRSTRFGRHSLAIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQP 227 Query: 238 LAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDG-----TLSSWW 292 GVG EL AI++VV+GGTLL+GG G++ T+ GV + GL+ +NF+ +LS++W Sbjct: 228 NEGVGWELFAISAVVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYW 287 Query: 293 TKIAIGILLFIFIALQ 308 + G+ L + I LQ Sbjct: 288 QSVIRGVFLLLVIVLQ 303 Lambda K H 0.329 0.145 0.428 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: 309 Number of extensions: 20 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: 331 Length of database: 321 Length adjustment: 28 Effective length of query: 303 Effective length of database: 293 Effective search space: 88779 Effective search space used: 88779 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: 48 (23.1 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