Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate PfGW456L13_3346 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3346 Length = 536 Score = 229 bits (583), Expect = 2e-64 Identities = 122/253 (48%), Positives = 173/253 (68%), Gaps = 1/253 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN-G 62 L+ V +L V F +AV+G+S+ + +GE+L +VGESGSGKSV+ S+LRL+ Sbjct: 6 LIEVRDLSVNFVVGNRCQRAVEGVSFDIKRGETLALVGESGSGKSVTAHSILRLLPYPLA 65 Query: 63 RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 R G ++ G++LL+L ++ +R+IRG I++IFQ PMTSLNP+ + Q+ E + H+ Sbjct: 66 RHPSGTILYSGQNLLELKEKTIRHIRGNRIAMIFQEPMTSLNPLHSIEKQINEVLGIHKG 125 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 + + A +R +ELLE VGIPE KR P + SGG RQRVMIAMALA P+LLIADEPT Sbjct: 126 LTGKVATKRTLELLEMVGIPEPHKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPT 185 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVT+Q +I+ELL+EL+ GM+++ I+HDL++ R+ M G IVE+A EE+ Sbjct: 186 TALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQQGCIVEQASCEEL 245 Query: 243 LKTPLHPYTKGLL 255 + P HPYT+ LL Sbjct: 246 FRAPQHPYTRELL 258 Score = 180 bits (456), Expect = 8e-50 Identities = 107/262 (40%), Positives = 164/262 (62%), Gaps = 17/262 (6%) Query: 4 LLNVNNLKVEFHRVEGI-------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 LL V +LKV F +G+ VKAVDGI++ L +G++LGIVGESGSGKS L++LR Sbjct: 275 LLAVEDLKVWFPIKKGLLKRTVDYVKAVDGINFSLPQGQTLGIVGESGSGKSTLGLAILR 334 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 LI G I F G+ L L ++++R +R +++ ++FQ+P SL+P + V V E Sbjct: 335 LIASKGAIR-----FEGQQLDCLTQQQVRPLR-REMQVVFQDPFGSLSPRMCVSQIVGEG 388 Query: 117 IIWHRLMKNEEARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKL 175 + H++ E + I L+ VG+ PE+ R YP +FSGG RQR+ IA AL P L Sbjct: 389 LRIHKMGTEAEQEQAIIAALKEVGLDPETRHR---YPHEFSGGQRQRIAIARALVLKPAL 445 Query: 176 LIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVE 235 ++ DEPT+ALD T+Q Q++ELL+ L+ +Y ++ +FI+HDL+V +++ + G++VE Sbjct: 446 ILLDEPTSALDRTVQRQVVELLRSLQTKYNLTYLFISHDLAVVKALSHQLMVVKHGQVVE 505 Query: 236 EAPVEEILKTPLHPYTKGLLNS 257 + + I P HPYT+ LL + Sbjct: 506 QGDAQSIFAAPQHPYTQQLLEA 527 Lambda K H 0.320 0.139 0.401 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: 445 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 536 Length adjustment: 31 Effective length of query: 293 Effective length of database: 505 Effective search space: 147965 Effective search space used: 147965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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