GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  189 bits (480), Expect = 1e-52
 Identities = 126/362 (34%), Positives = 194/362 (53%), Gaps = 24/362 (6%)

Query: 1   MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60
           ++L LD+++K++G    L D+SL + +G   V +G +  GK++L+R++AGLD+   G + 
Sbjct: 2   IKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61

Query: 61  VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLR--GEKNIDARVREIASRL 118
           +DG+ V  +  R+R V MV+Q +  YP M V  NI+  LKL    + ++  RV + A  L
Sbjct: 62  IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQIL 121

Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178
            +D  L R P ELSGGQ+QRVA+ RA+A+   ++L DEPL NLD  LR ++R E+ +L  
Sbjct: 122 QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHD 181

Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238
              ST++Y T +  EA+ L     VL+ G++ Q G   E++  P S  VA     P MN 
Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNF 241

Query: 239 MAASATAQGVRLQGGAELTL---------PLP---QGAATAAGLTVGVRASALRVHARPG 286
           ++A       RLQ   E +L          LP      A    L++G+R   + + A  G
Sbjct: 242 LSA-------RLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADG 294

Query: 287 DVSVAGVVELAEISGSDTFVHASTPWGD-LVAQLTGVHYFELGTAITLHLDPAQAYVFGA 345
              V  VV   E  GS+T+VH  T   + L+ +      ++ G  + L LD    ++F A
Sbjct: 295 TAGV--VVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDA 352

Query: 346 DG 347
           DG
Sbjct: 353 DG 354


Lambda     K      H
   0.318    0.133    0.375 

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: 300
Number of extensions: 13
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: 363
Length of database: 381
Length adjustment: 30
Effective length of query: 333
Effective length of database: 351
Effective search space:   116883
Effective search space used:   116883
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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