GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Halococcus hamelinensis 100A6

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate WP_007693924.1 C447_RS11155 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>NCBI__GCF_000336675.1:WP_007693924.1
          Length = 368

 Score =  314 bits (804), Expect = 3e-90
 Identities = 184/372 (49%), Positives = 238/372 (63%), Gaps = 25/372 (6%)

Query: 1   MAKVRLEHVWKRF----GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEIS 56
           M ++ +  + K +      +VAV+D +L  EDGEF+VFVGPSGCGK+TTLR IAGLE ++
Sbjct: 1   MTQIEINELTKEYDTGDSAIVAVEDLDLSIEDGEFIVFVGPSGCGKSTTLRCIAGLESVT 60

Query: 57  EGNIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLR-RYPKDEIDRRVK 115
           +G I   D +VND+ P+DRD+AMVFQNYALYPHM V +NM+FGL+L  +    EID RV 
Sbjct: 61  DGEIRFDDEVVNDLRPRDRDVAMVFQNYALYPHMTVKQNMSFGLKLSSQLSSGEIDSRVT 120

Query: 116 EAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAE 175
           +AA ++ I+ LL ++P ELSGGQ+QRVA+GR+IVREP VFLMDEPLSNLDAKLR  MR E
Sbjct: 121 DAAEMMGIDDLLGKRPGELSGGQQQRVALGRSIVREPGVFLMDEPLSNLDAKLRAGMRTE 180

Query: 176 IAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIG 235
           I +LQ  L VTTIYVTHDQ EAM +G RI V+  G +QQ   P  LY  P N FVA FIG
Sbjct: 181 IQELQNELDVTTIYVTHDQTEAMAMGDRIAVLNGGVLQQAAVPEELYRNPVNEFVADFIG 240

Query: 236 SPSMNFVRAGVEVQGEKVYLVAP-GFRIRANAV-LGSALKPYAGKEVWLGVRPEHLGLKG 293
           SPS+N     V V+G +  L  P GF  R +   LG            +GVRPE L    
Sbjct: 241 SPSINLF--DVTVEGTR--LAGPGGFTYRLSGFDLGER------SHARMGVRPEDL---- 286

Query: 294 YTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQR 353
              I E  + L   V VVE +G E  I+  + G  +VA+ D     +P D+V L  + + 
Sbjct: 287 --AIDERGDDL--TVTVVEKMGNENFIYGELGGQEVVARTDSSIRPEPDDEVGLAFEEEA 342

Query: 354 LHAFDLETDRTI 365
           ++ F+ ++ R I
Sbjct: 343 VYFFEPDSGRAI 354


Lambda     K      H
   0.320    0.139    0.400 

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: 396
Number of extensions: 19
Number of successful extensions: 3
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: 368
Length adjustment: 30
Effective length of query: 346
Effective length of database: 338
Effective search space:   116948
Effective search space used:   116948
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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