GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          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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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