GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD 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 GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__psRCH2:GFF3591
          Length = 369

 Score =  241 bits (614), Expect = 3e-68
 Identities = 141/317 (44%), Positives = 187/317 (58%), Gaps = 14/317 (4%)

Query: 14  GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPK 73
           G+ + V+D NL+   GEF+  +GPSG GKTT+L M+AG E  + G I +  R +N+VPP 
Sbjct: 22  GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRAINNVPPH 81

Query: 74  DRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKIEHLLNRKPRE 133
            RD+ MVFQNYAL+PHM V EN+AF L +R   K +I  RVK A  ++++E   NR P +
Sbjct: 82  KRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEGFRNRYPAQ 141

Query: 134 LSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHD 193
           LSGGQ+QRVA+ RA+V EP++ LMDEPL  LD +LR +M+ EI  L  RLGVT +YVTHD
Sbjct: 142 LSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVTVVYVTHD 201

Query: 194 QVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGS----PSMNFVRAGVEVQ 249
           Q EA+T+  R+ V   G+IQQ++ P  LY+ P N FVA F+G     P+    R G    
Sbjct: 202 QGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGENNRLPAHLLDRRG---- 257

Query: 250 GEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVE 309
                 +  G  + A AV   A    AG  V L +RPE + L G +      N   G V 
Sbjct: 258 DSCTVKLGRGETVEALAVNVGA----AGTPVSLSIRPERVLLNGASA--NCPNRFTGRVA 311

Query: 310 VVEPLGAETEIHVAVNG 326
               LG    I + V G
Sbjct: 312 EFIYLGDHIRIRLEVCG 328


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: 367
Number of extensions: 20
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: 369
Length adjustment: 30
Effective length of query: 346
Effective length of database: 339
Effective search space:   117294
Effective search space used:   117294
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