GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c07320 in Pseudomonas fluorescens GW456-L13

Align Inositol transport system ATP-binding protein (characterized)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= reanno::Phaeo:GFF717
         (261 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 517

 Score =  128 bits (321), Expect = 3e-34
 Identities = 79/248 (31%), Positives = 126/248 (50%), Gaps = 7/248 (2%)

Query: 1   MSMSQP--LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHK 58
           MS+  P  ++ + GI K +   + LAG+ + +  GE   L G+NGAGKST  K + G+  
Sbjct: 1   MSVCAPNAVLSVSGIGKTYAQPV-LAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVT 59

Query: 59  PTKGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKL 118
           PT G + ++GQ         A A GI  V Q L ++P +SV+ N F+ N P +       
Sbjct: 60  PTTGQMQYQGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKG----GW 115

Query: 119 FDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSA 178
                  +  +E M  +G++   PD  VG L  G +Q V IAR +     VLILDEPT+ 
Sbjct: 116 ISRKQLRKAAIEAMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAM 175

Query: 179 LGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAE 238
           L  R+   +   I +++ +GV++++I+H +     V  R  VL  G  +      + ++E
Sbjct: 176 LTAREVEMLFEQITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSE 235

Query: 239 ELQDMMAG 246
           +L  +M G
Sbjct: 236 QLVTLMVG 243



 Score = 90.5 bits (223), Expect = 6e-23
 Identities = 62/220 (28%), Positives = 103/220 (46%), Gaps = 7/220 (3%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF--EGQPLHFADPRDAIAAG 83
           VS +V  GE   + G  GAG++  ++ + G      G I      Q ++   P DA+  G
Sbjct: 276 VSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIALGAPAQVINVRSPVDAVGHG 335

Query: 84  IATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLR 140
           IA + +      ++   S+  N  +GN P   I      D+D    +   ++  M I   
Sbjct: 336 IALITEDRKGEGLLLTQSIGANIALGNMP--GISGAGFVDNDKERALAQRQIDAMRIRSS 393

Query: 141 GPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVA 200
           GP Q V  LSGG +Q V I R +     VL+ DEPT  + V    ++   + ++ +QG A
Sbjct: 394 GPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDEPTRGIDVGAKFDIYNLLGELTRQGKA 453

Query: 201 VVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240
           +V ++ ++R  + + DR  VL+ G  + T  R   + +EL
Sbjct: 454 LVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDSWTQDEL 493


Lambda     K      H
   0.321    0.137    0.395 

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: 322
Number of extensions: 24
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 517
Length adjustment: 30
Effective length of query: 231
Effective length of database: 487
Effective search space:   112497
Effective search space used:   112497
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 (21.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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