GapMind for catabolism of small carbon sources

 

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

Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate AO353_16120 AO353_16120 D-alanine/D-serine/glycine permease

Query= uniprot:Q4KIP0
         (466 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16120
          Length = 472

 Score =  399 bits (1024), Expect = e-115
 Identities = 208/465 (44%), Positives = 292/465 (62%), Gaps = 15/465 (3%)

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
           E+P W+ A    V +  IN++ VK FGE EFWFA+IK+V I+ M+V G  ++  G G  G
Sbjct: 131 EVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVGGVGVIAFGFGNDG 190

Query: 181 SQASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQV 240
               +SNLWSHGGF PNG  G+LM++  +MF++ G+E++G+TA EA  P+K IP AI  V
Sbjct: 191 VALGISNLWSHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 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 ITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAK-TSNGVPRRALLLSIGALLLGVLLNY 360

Query: 361 LAPHEALELLFALVVAALMINWALISLTHLRFRKAM--AEQGVVPSFKAFWSPLSNYLCL 418
           L P +    + A+     +  W +I L  L+FRK +  AE+  +  ++ +  P+S+YL L
Sbjct: 361 LVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSPAERAAL-KYRMWLYPVSSYLAL 419

Query: 419 AFMVMIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKKASQP 463
           AF+VM+VG+M   P  R ++Y  P +++++   + + + +    P
Sbjct: 420 AFLVMVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGVP 464


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: 750
Number of extensions: 46
Number of successful extensions: 5
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: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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