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_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  137 bits (346), Expect = 3e-37
 Identities = 76/240 (31%), Positives = 129/240 (53%), Gaps = 6/240 (2%)

Query: 8   IRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFE 67
           +R  GI K F  V AL  +S    PG+ H L+G+NGAGKST +K + G + P  G +   
Sbjct: 16  LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75

Query: 68  GQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRI 127
            + + F    D+I +G+A +HQ L ++P M+V+ N F+G+ P        L +     + 
Sbjct: 76  ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLP----ASFGLINRSTLRQQ 131

Query: 128 TMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANV 187
            +  ++ +   +  P + VG LS G+RQ V IA+A+  GA V+  DEPTS+L  R+   +
Sbjct: 132 ALACLKGLADEI-DPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRL 190

Query: 188 LATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGT-AQRGDISAEELQDMMAG 246
           +A I ++R +G  V++++H +     + +  TV   G+ + T      ++ ++L   M G
Sbjct: 191 MAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVG 250



 Score = 92.0 bits (227), Expect = 2e-23
 Identities = 64/223 (28%), Positives = 109/223 (48%), Gaps = 15/223 (6%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85
           VS +V  GE   L G  GAG++  ++ +SG+ + + G +   G  L    PRDAIAAGI 
Sbjct: 283 VSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGIL 342

Query: 86  TVHQHL---AMIPLMSVSRNFFMGNEPIRK-IGPLK--LFDHDYANRITMEEMRKMGINL 139
              +      ++PL SV+ N  +         G L   L++ D A     ++++ + +  
Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAE----QQIKALKVKT 398

Query: 140 RGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGV 199
               Q +  LSGG +Q   + R +    KVL+LDEPT  + +   A +   I  +  +G+
Sbjct: 399 PNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGI 458

Query: 200 AVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242
           AV+ ++ ++   + + DR  VL  G     A RG++S E+  +
Sbjct: 459 AVIVVSSDLMEVMGISDRILVLCEG-----ALRGELSREQANE 496


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: 339
Number of extensions: 18
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: 261
Length of database: 514
Length adjustment: 29
Effective length of query: 232
Effective length of database: 485
Effective search space:   112520
Effective search space used:   112520
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