GapMind for catabolism of small carbon sources

 

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

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::B8H229
         (515 letters)



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

 Score =  386 bits (991), Expect = e-111
 Identities = 219/488 (44%), Positives = 312/488 (63%), Gaps = 9/488 (1%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           + K+FPGV+ALD +  V   G+VHAL+GENGAGKSTL+KIL  A+   +G +    + +D
Sbjct: 21  IGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTMD 80

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128
            +         G+A I+QE +L PE++VAEN++LG  P   GL++ S LR  A A L  L
Sbjct: 81  FKSTADSIGS-GVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGL 139

Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188
              ++P   V  L++ ++Q+VEIAKA++  A +I  DEPT++LS RE+DRL AII  L+ 
Sbjct: 140 ADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRD 199

Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFERRK 247
               V+YVSHR+ EV  +C+  TV +DGR+V +  D++ +    +V  MVGR ++     
Sbjct: 200 EGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQDIYDY 259

Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307
           R R  GAV LKV+G       L  PG    VSF    GEI+GL GLVGAGRT+L RL+ G
Sbjct: 260 RPRQRGAVALKVDG-------LLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSG 312

Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367
               +AG++ +    L+LRSPRDAI AGI+L PEDRK++G     S+  N+++ +  A S
Sbjct: 313 LARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHS 372

Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427
             G  +    E+D  E   + L++K  +A   I  LSGGNQQK +LGR +++  KVL++D
Sbjct: 373 TFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432

Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487
           EPTRGIDIGAKAE++Q++ +LA  G+AV+V+SS+L EVM +SDRI+V  EG +  +L  +
Sbjct: 433 EPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSRE 492

Query: 488 TATEEGLM 495
            A E  L+
Sbjct: 493 QANESNLL 500



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 63/258 (24%), Positives = 110/258 (42%), Gaps = 32/258 (12%)

Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316
           L+  G+    P + A   L  +SF A  G++  L G  GAG++ L +++ GA    +G +
Sbjct: 16  LRFNGIGKTFPGVKA---LDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGAL 72

Query: 317 LVDDKPLRLRSPRDAIQAGIM-------LVPEDRKQQGCFLDHSIRR----NLSLPSLKA 365
            + ++ +  +S  D+I +G+        LVPE    +  FL H        N S    +A
Sbjct: 73  QIGERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQA 132

Query: 366 LSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLI 425
           L+ L    DE                   D +  +G+LS G +Q V + +A++    V+ 
Sbjct: 133 LACLKGLADE------------------IDPQEKVGRLSLGQRQLVEIAKALSRGAHVIA 174

Query: 426 VDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLD 485
            DEPT  +       +  ++  L D G  V+ +S  + EV  + + + VF++G  V   D
Sbjct: 175 FDEPTSSLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFD 234

Query: 486 AQTATEEGLMAYMATGTD 503
             +      +     G D
Sbjct: 235 DMSQLTHDQLVTCMVGRD 252


Lambda     K      H
   0.320    0.136    0.380 

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: 690
Number of extensions: 30
Number of successful extensions: 8
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: 515
Length of database: 514
Length adjustment: 35
Effective length of query: 480
Effective length of database: 479
Effective search space:   229920
Effective search space used:   229920
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 (21.8 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