GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Azospirillum brasilense Sp245

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 AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__azobra:AZOBR_RS30410
          Length = 371

 Score =  275 bits (703), Expect = 1e-78
 Identities = 170/364 (46%), Positives = 225/364 (61%), Gaps = 21/364 (5%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           VR++ V   +G    +KD +L+ + GEF  F+GPSGCGKTT LR+IAG      G + IG
Sbjct: 19  VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
            R ++ +P   RD+ MVFQ+YAL+PHM V  N+AFGL  RR P+ EI+RRV  A  ++ +
Sbjct: 79  GRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGL 138

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
           +HL +R+P +LSGGQ+QRVA+ R IV EPKV L+DEPLSNLDAKLRV+MR E+  LQR+L
Sbjct: 139 KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKL 198

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSM--NF 241
           G+TTI+VTHDQ EA T+  RI VM+DG +QQV TP  LYD PAN FVAGF+G+ ++    
Sbjct: 199 GLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGTANVLEGQ 258

Query: 242 VRAGVEVQGEKVYLVAPGFRIRANAVLGSALKP-YAGKEVWLGVRPEHLGLKGYTTIPEE 300
           VRA   V G   +++  G  I     L   ++P  AGK   L  RP++L ++     P  
Sbjct: 259 VRA---VDGGTAFVMGGGVPI----PLPHGVEPGAAGK---LMFRPQNLFIRQDGGPPRA 308

Query: 301 ENV-LRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDL 359
            +V L G V   E LGA     V + G     +V   AP + GD    L  T      DL
Sbjct: 309 GHVRLMGVVRHREFLGASIRYAVDIGG----QQVQVDAPHQAGD---ALLPTDTPITLDL 361

Query: 360 ETDR 363
             D+
Sbjct: 362 AADK 365


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: 379
Number of extensions: 15
Number of successful extensions: 1
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: 371
Length adjustment: 30
Effective length of query: 346
Effective length of database: 341
Effective search space:   117986
Effective search space used:   117986
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.

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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