GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TT_C0327 in Pseudomonas fluorescens FW300-N1B4

Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate Pf1N1B4_595 Glucose ABC transport system, inner membrane component 1

Query= TCDB::Q72KX3
         (369 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_595 Glucose ABC transport
           system, inner membrane component 1
          Length = 314

 Score =  115 bits (288), Expect = 2e-30
 Identities = 77/242 (31%), Positives = 129/242 (53%), Gaps = 29/242 (11%)

Query: 152 SFPWLATREQVLVFDWNR-------LPFYTALVVGLVLLYVAYTAYREGERRRA------ 198
           S+ W+  ++ + + D +R       L  +  + +G+ L+   + A    +R R       
Sbjct: 68  SYKWVGLQQYIRLMDNDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRT 127

Query: 199 --LWGLASA----GVLLLWAFAFGQGL-RLLPYPEVHGFSL--------ALVGVILAAVW 243
             L+ +A +    G    W    G GL ++L      GF L         +  +++AAVW
Sbjct: 128 VYLYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVW 187

Query: 244 QMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIAL 303
           Q SG+ MA++LAGLRG+   ++ AA+VDGAS   ++ +++ P L P+  SA ++L HIA+
Sbjct: 188 QASGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAI 247

Query: 304 KIFDLVFAM-AGLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQ 362
           K FDLV AM AG     +D+PA++MY   F   Q   G+A  +++L  +  ++VPYL ++
Sbjct: 248 KSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMMMLGAILAILVPYLYSE 307

Query: 363 LR 364
           LR
Sbjct: 308 LR 309



 Score = 92.4 bits (228), Expect = 1e-23
 Identities = 60/160 (37%), Positives = 88/160 (55%), Gaps = 11/160 (6%)

Query: 4   RILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYRELF 63
           R L  LVL PS+L V V  YG+I     +S T+         +  P  ++VGL+ Y  L 
Sbjct: 30  RWLPKLVLAPSMLIVLVGFYGYIIWTFVLSFTN--------SSFMPSYKWVGLQQYIRLM 81

Query: 64  TGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFV 123
               + R+  +  NL  F   F+  SL LG+ LA+ +D+  R EGF RTV+L+PMALS +
Sbjct: 82  D---NDRWWVASKNLAVFGGMFIGISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMI 138

Query: 124 VTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVL 163
           VTGT W+WLL P  G++ +   +G       WL  +++V+
Sbjct: 139 VTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVV 178


Lambda     K      H
   0.331    0.146    0.458 

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: 379
Number of extensions: 13
Number of successful extensions: 4
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: 369
Length of database: 314
Length adjustment: 28
Effective length of query: 341
Effective length of database: 286
Effective search space:    97526
Effective search space used:    97526
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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, the preprint on GapMind for carbon sources, 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