GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas stutzeri RCH2

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 GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__psRCH2:GFF1860
          Length = 390

 Score =  312 bits (799), Expect = 1e-89
 Identities = 173/379 (45%), Positives = 236/379 (62%), Gaps = 20/379 (5%)

Query: 1   MAKVRLEHVWKRFG--KVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEG 58
           MA + L +V K +G  ++  +KD  L+ + GEF++ VGPSGCGK+T +  IAGLE I+ G
Sbjct: 1   MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60

Query: 59  NIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAA 118
            I +    ++   PKDRDIAMVFQ+YALYP M+V +N+AFGL++R+ P  +I+  V   A
Sbjct: 61  EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120

Query: 119 RILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAK 178
           ++L+IE LL RKP +LSGGQ+QRVAMGRA+ R PK++L DEPLSNLDAKLRVEMR EI  
Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180

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

Query: 239 MNFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKP--------YAGKEVWLGVRPEHLG 290
           MNFV   +  +  +   V        N+  GS   P           +E+ LG+RPE +G
Sbjct: 241 MNFVPLRIRQRDGRWVGV-------LNSEQGSCELPLPITSDDGLRDRELILGIRPEQIG 293

Query: 291 LKGYTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLAD 350
           L         +  L  ++EVVEP G +T +   +N      ++      + G+ + L  D
Sbjct: 294 L---APAGSADFSLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFD 350

Query: 351 TQRLHAFDLETDRTIGHAQ 369
            +R   FD +T   +G  Q
Sbjct: 351 PRRALLFDAQTGERLGVVQ 369


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: 407
Number of extensions: 15
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: 390
Length adjustment: 30
Effective length of query: 346
Effective length of database: 360
Effective search space:   124560
Effective search space used:   124560
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