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 WP_015331619.1 FAES_RS12700 ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_000331105.1:WP_015331619.1 Length = 225 Score = 112 bits (280), Expect = 8e-30 Identities = 80/232 (34%), Positives = 116/232 (50%), Gaps = 13/232 (5%) Query: 5 LNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 L V+NL + + + +S+ L G++ IVG SGSGK+ +LL L R Sbjct: 3 LRVDNLTKTYQSAGQTLTVLHDVSFSLQPGDTFAIVGPSGSGKT----TLLGLCAGLDRA 58 Query: 65 VDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMK 124 G G L LN+++ +R + + IFQN L P + VM P+ L Sbjct: 59 TSGSVWLNGVQLDTLNEDQRAAVRNQHVGFIFQN--FQLLPTLTALENVMVPL---ELRG 113 Query: 125 NEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTA 184 A A +LL+RVG+ R +YP Q SGG +QRV +A A + P +L ADEPT Sbjct: 114 QRGAERIARDLLDRVGLGN---RSHHYPLQLSGGEQQRVSLARAFSNRPAILFADEPTGN 170 Query: 185 LDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 LD A + LL EL E G +++ +THDL +A R+I + G +VE+ Sbjct: 171 LDEDTSATVENLLFELNREAGTTLVVVTHDLELAAK-TGRMIRIRGGHVVED 221 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: 117 Number of extensions: 4 Number of successful extensions: 2 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: 324 Length of database: 225 Length adjustment: 25 Effective length of query: 299 Effective length of database: 200 Effective search space: 59800 Effective search space used: 59800 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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