GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens FW300-N2C3

Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate AO356_17670 AO356_17670 D-alanine/D-serine/glycine permease

Query= uniprot:Q4KIP0
         (466 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17670 AO356_17670
           D-alanine/D-serine/glycine permease
          Length = 473

 Score =  400 bits (1029), Expect = e-116
 Identities = 201/449 (44%), Positives = 288/449 (64%), Gaps = 12/449 (2%)

Query: 3   QTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 62
           +T + G LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y I G    +IM
Sbjct: 11  ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70

Query: 63  RQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWP 122
           R LGEM V  PVAGSFS +A  Y G   GFL GWNYW L+++  +AE+TAV  Y+  W+P
Sbjct: 71  RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFP 130

Query: 123 EIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSGSG--G 180
           ++P W+ A    V +  IN++ VK FGE EFWFA+IK+V I+ M++ G  ++  G G  G
Sbjct: 131 DVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDG 190

Query: 181 SQASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQV 240
               +SNLW+HGGF PNG +G+LM++  +MF++ G+E++G+TA EA  P+K IP AI  V
Sbjct: 191 VALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250

Query: 241 VYRVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVV 300
            +R+L+FYVGAL V+LS+YPW+E+             SPFV  F  +G   AA I+NFVV
Sbjct: 251 FWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVV 301

Query: 301 LTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNY 360
           +TAALS  N G++   RMLY LA+ G AP    K +  GVP  AL +S    LL VL+NY
Sbjct: 302 ITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNY 361

Query: 361 LAPHEALELLFALVVAALMINWALISLTHLRFRKAM-AEQGVVPSFKAFWSPLSNYLCLA 419
           L P +    + ++     +  W +I L  L+FRK++ A +     ++ +  P+S+YL LA
Sbjct: 362 LVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALA 421

Query: 420 FMVMIVGVMWMIPGIRASVYAIPVWVLVI 448
           F+V++VG+M   P  R ++Y  P +++++
Sbjct: 422 FLVLVVGLMAYFPDTRVALYVGPAFLVLL 450


Lambda     K      H
   0.327    0.141    0.440 

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: 738
Number of extensions: 41
Number of successful extensions: 4
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: 466
Length of database: 473
Length adjustment: 33
Effective length of query: 433
Effective length of database: 440
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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