Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 316 bits (810), Expect = 5e-91 Identities = 186/375 (49%), Positives = 237/375 (63%), Gaps = 26/375 (6%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA ++ +D SY G + + +LEIADGEF+V+VGPSGCGKST LRM+AGLE +T G Sbjct: 1 MAEISLRDVRKSYSGLE--VIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAG 58 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 I IG + V + PR+RDIAMVFQNYALYPHMTV ENM + L+IA S+ EI +RV +A Sbjct: 59 EIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSA 118 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L + L+RKP+ LSGGQRQRVAMGRA+VRNP FL+DEPLSNLDAKLRVQ R QI Sbjct: 119 KMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKE 178 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 LQR + T++YVTHDQ EA+T+ DR+ V+ G +Q+ P E+YDRPA FVAGFIGSPA Sbjct: 179 LQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPA 238 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300 MN+ + GDA ++++ + LA P I +G RPE L P G + Sbjct: 239 MNM-LPARGLGDA------LEVAGQRLAVPAPAGRDLI-LGIRPEHLH--PAGPE-EPGF 287 Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIV 360 + + VE LG+D+F +G L DL + G+ VR AP + Sbjct: 288 ELHVQAVEWLGADAFAHGSLADGTDL-----VLRTPGKAPVRERDRLKVAPDA------- 335 Query: 361 EGGQHNFSASTGKRL 375 H F A TG+RL Sbjct: 336 -AALHLFDAGTGRRL 349 Lambda K H 0.316 0.135 0.380 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: 389 Number of extensions: 17 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: 376 Length of database: 349 Length adjustment: 29 Effective length of query: 347 Effective length of database: 320 Effective search space: 111040 Effective search space used: 111040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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