Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= SwissProt::P37772 (331 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 148 bits (373), Expect = 2e-40 Identities = 110/307 (35%), Positives = 169/307 (55%), Gaps = 15/307 (4%) Query: 4 RNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDL 63 R L L + IG VL L P F + I NIL + +GI+++GMTFVIL+GGIDL Sbjct: 35 RMLGLALVIGA-VLSLLS-----PYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDL 88 Query: 64 SVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAG 123 SVGSV +G+ L + D+ + +A L ++ G G G+LI ++ AF++TL Sbjct: 89 SVGSVAGLSGIVLGLALKDYPIP--VAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGM 146 Query: 124 MFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRT 183 M R ++Y+ S ++ P LSS+ + G + + L A ++ +L + T Sbjct: 147 MAIGRSLAYIFSGQTAISGFP--SDLSSIVYTDVFGIPTNVL-FLGFAYLLAWGYLTY-T 202 Query: 184 RFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGY-ALAGVG 242 + G +YAIG N +A G+ +I Y++S LA +A I FS+ L G G Sbjct: 203 KGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVA-ITFSVAQILSVDPLTGNG 261 Query: 243 VELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLF 302 +ELDAIA+VVIGG L GG G+++GTL GV I +I+ +N G +S +W AIG ++ Sbjct: 262 MELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLG-VSPFWQGSAIGSIII 320 Query: 303 IFIALQR 309 + + ++R Sbjct: 321 MALLVER 327 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: 350 Number of extensions: 36 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: 331 Length of database: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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