GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1897 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1897
          Length = 386

 Score =  327 bits (837), Expect = 4e-94
 Identities = 176/373 (47%), Positives = 244/373 (65%), Gaps = 10/373 (2%)

Query: 1   MAKVRLEHVWKRFGKVV--AVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEG 58
           MA + L +V K +G  +   +K+  L+ +DGEF++ VGPSGCGK+T +  IAGLE IS G
Sbjct: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60

Query: 59  NIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAA 118
            I + D  ++ + PKDRDIAMVFQ+YALYP M+V +N+AFGL++R+ P  EID  V   +
Sbjct: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120

Query: 119 RILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAK 178
           ++L+IEHLL+RKP +LSGGQ+QRVAMGRA+ R PK++L DEPLSNLDAKLRVEMR E+  
Sbjct: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPS 238
           + +RL  TT+YVTHDQ+EAMTLG ++ VMKDG IQQ  TP ++Y+ PAN FVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240

Query: 239 MNFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIP 298
           MNF+   ++ +  ++  +    + R    LG        +EV LG+RPE + L       
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILAN----- 295

Query: 299 EEEN---VLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLH 355
            E N    +R EV+V EP G +T + V +N T +  ++        G+ + L  D  ++ 
Sbjct: 296 GEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVL 355

Query: 356 AFDLETDRTIGHA 368
            FD +T   +G A
Sbjct: 356 LFDAKTGERLGVA 368


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: 416
Number of extensions: 22
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: 386
Length adjustment: 30
Effective length of query: 346
Effective length of database: 356
Effective search space:   123176
Effective search space used:   123176
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