GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS34245 in Pseudomonas fluorescens GW456-L13

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:B2T9V9
         (510 letters)



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

 Score =  255 bits (652), Expect = 2e-72
 Identities = 169/475 (35%), Positives = 254/475 (53%), Gaps = 13/475 (2%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           + K F    AL+++S    PG+ HAL+G NGAGKSTL+ IL G   P +G ++       
Sbjct: 21  IGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTMD 80

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK 139
             +  D+    VA ++Q   ++ +++VAENLF+   P   G+I+   +R+ A A L    
Sbjct: 81  FKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGLA 140

Query: 140 IDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQRE 199
            ++    + G LS+  RQLVEIA+ALS GA  I  DEPT+ L   EI RL   I  L+ E
Sbjct: 141 DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDE 200

Query: 200 GVTFLFISHHLQEVYEICQAVTVLRDARHI-VSAPVSALPREQLIEAMTGERGGLAVADA 258
           G   L++SH ++EV+ IC AVTV +D R++     +S L  +QL+  M G R    + D 
Sbjct: 201 GKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVG-RDIQDIYDY 259

Query: 259 AARGALPADTAVALELKELTGADY-EGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317
             R       AVAL++  L G    E VSF V +GE++GL G   +GRT +   ++GL  
Sbjct: 260 RPR----QRGAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSGLAR 315

Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377
              G + + G  L       ++A GI   P+DR  EG++   SVAEN +++       FG
Sbjct: 316 HSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFG 375

Query: 378 IAAPA---KKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLID 434
                   K NA  ++ I AL +        +  LSGGNQQK ++ R L+    VL+L +
Sbjct: 376 CLLRGLWEKDNA--EQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDE 433

Query: 435 PTAGVDVKSKEALLSVVDRVREEGKAVLVVSGEL-DDLRTCDRVLVMFRGRVAAE 488
           PT G+D+ +K  +  ++  +  EG AV+VVS +L + +   DR+LV+  G +  E
Sbjct: 434 PTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGE 488


Lambda     K      H
   0.318    0.134    0.377 

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: 569
Number of extensions: 41
Number of successful extensions: 7
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: 510
Length of database: 514
Length adjustment: 35
Effective length of query: 475
Effective length of database: 479
Effective search space:   227525
Effective search space used:   227525
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: 52 (24.6 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