Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate PfGW456L13_5057 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5057 Length = 322 Score = 206 bits (525), Expect = 5e-58 Identities = 116/301 (38%), Positives = 176/301 (58%), Gaps = 10/301 (3%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG----GKIFFEGKDIT 82 K VDG+ +++ +GE L +VGESG GKS ++ L+ G + F+GK++ Sbjct: 16 KNATPVVDGLDLQVDKGEVLAIVGESGSGKSVTMMALMGLIEHPGIVTADALNFDGKNML 75 Query: 83 NLNDKEMKPY-RKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLD 141 LN+++ + K + ++FQDP+ +LNP TVG IE+ L +H + K RKR ELL+ Sbjct: 76 KLNNRQRRQIVGKDLSMVFQDPMTALNPSYTVGFQIEEVLRLHLKMSGKAARKRAIELLE 135 Query: 142 MVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLL 199 V I ++++PH+ SGG QR+ IA A+A PK ++ DEP +ALDV+IQAQI+DLL Sbjct: 136 KVEIPGAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPTTALDVTIQAQIMDLL 195 Query: 200 EEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKS 259 +Q++ + + I H+LAVV + +V VMY G+ VE G V ++F P HPY+ ALLK+ Sbjct: 196 LALQKEQNMGLVLITHDLAVVAETAQRVCVMYAGQAVEVGQVPQLFDIPAHPYSEALLKA 255 Query: 260 VPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVS 319 +P+ R +L G +P D P+GC RC K C ++ P L + + N Sbjct: 256 IPEHSLGA--SRLSTLPGIVPGRYDRPQGCLLSPRCPYVKDNCRQQRPALDQ-KSNSLAR 312 Query: 320 C 320 C Sbjct: 313 C 313 Lambda K H 0.321 0.142 0.417 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: 285 Number of extensions: 10 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: 328 Length of database: 322 Length adjustment: 28 Effective length of query: 300 Effective length of database: 294 Effective search space: 88200 Effective search space used: 88200 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: 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