GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens FW300-N2E3

Align L-alanine and D-alanine permease (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05965
          Length = 466

 Score =  407 bits (1046), Expect = e-118
 Identities = 207/462 (44%), Positives = 295/462 (63%), Gaps = 15/462 (3%)

Query: 11  ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70
           E  Q G LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y I G    +IM
Sbjct: 4   EQLQQGVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 63

Query: 71  RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFP 130
           R LGEM V  PVAGSFS +A +Y G  AGFL+GWNYW L+++  +AE+TAV  Y+  W+P
Sbjct: 64  RQLGEMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWP 123

Query: 131 DVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDG 190
           +VP W+ A    V +  IN + VK FGE EFWFA+IK+V II M+  G  ++  G G  G
Sbjct: 124 EVPTWVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTG--G 181

Query: 191 VALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250
               +SNLW+HGGF PNG +G+LM++  +MF++ G+E++G+TA EA  P+K IP AI  V
Sbjct: 182 PQASVSNLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQV 241

Query: 251 FWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVV 301
            +R+L+FYVGAL V+LS+YPW+++            GSPFV  F  +G  TAA I+NFVV
Sbjct: 242 VYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVV 301

Query: 302 ITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNY 361
           +TAALS  N G++   RMLY LA+ G AP    K +  GVP RAL +S    +L V++NY
Sbjct: 302 LTAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNY 361

Query: 362 LVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALK-YRMWLYPVSSYLAL 420
           + P +    + ++     +  W MI L  LKFRK++   +R  +  ++ +  P ++YL L
Sbjct: 362 VAPNEALELLFALVVASLMINWAMISLTHLKFRKAM--GQRGIVPGFKAFWSPYTNYLCL 419

Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQPT 462
           AF+ +++ +M   P  R ++Y  P ++++L V FY  ++  T
Sbjct: 420 AFMAMIIYVMLLIPGVRASVYAIPVWVLILFV-FYRIRVART 460


Lambda     K      H
   0.328    0.142    0.444 

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: 666
Number of extensions: 35
Number of successful extensions: 3
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: 473
Length of database: 466
Length adjustment: 33
Effective length of query: 440
Effective length of database: 433
Effective search space:   190520
Effective search space used:   190520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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 (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