GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AGP1 in Pseudomonas simiae WCS417

Align general amino acid permease AGP1 (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter

Query= CharProtDB::CH_091105
         (633 letters)



>lcl|FitnessBrowser__WCS417:GFF4632 PS417_23700 aromatic amino acid
           transporter
          Length = 467

 Score =  219 bits (559), Expect = 2e-61
 Identities = 145/470 (30%), Positives = 235/470 (50%), Gaps = 30/470 (6%)

Query: 116 LKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQACGEM 175
           LK+ ++ RH+ +IALG  IGTGL +G+   L  AGP+ +++GYAI G I + I++  GEM
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFLIMRQLGEM 69

Query: 176 ALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTSVNPD 235
            +V   + G ++ +         GF   W Y + ++ V   EL      I++W   +   
Sbjct: 70  -IVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTW 128

Query: 236 VFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGFIGGK 295
           V  ++F+V V  IN    + + E EF+F   K++ + G  +LG  +   G G        
Sbjct: 129 VSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSN 188

Query: 296 YWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAAKQMI 354
            W   G F NG        G+  ++    F+FGG E + IT AE S PRK IP A  Q++
Sbjct: 189 LWSHGGFFPNGG------MGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVV 242

Query: 355 YRILFLFLATIILLGFLVPYNSD-QLLGSTGGGTKASPYVIAVASHGVRVVPHFINAVIL 413
           YRIL  ++  + +L  L P++   Q LG++G     SP+V   +  G     H +N V+L
Sbjct: 243 YRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVL 302

Query: 414 LSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAFCAASP 473
            + LS+ NS  Y ++R+   L+EQG APK    +++ G P+ A+ +SAL  ++       
Sbjct: 303 TAALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYV 362

Query: 474 KEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVW--GSAY 531
             +     L A+   S +  W  I ++H++FR+AM  QG +     FK+    W   S Y
Sbjct: 363 APQSALELLFALVVASLMINWALISITHIKFRKAMGEQGVT---PSFKT---FWFPFSNY 416

Query: 532 ACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIA-LYVGYKV 580
            C +  +++I    +AI  I           E+  AMP+ +  +YV Y++
Sbjct: 417 LC-LAFMVMIISVMLAIPGIS----------ESVYAMPVWVGIIYVAYRL 455


Lambda     K      H
   0.324    0.138    0.424 

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: 692
Number of extensions: 35
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: 633
Length of database: 467
Length adjustment: 35
Effective length of query: 598
Effective length of database: 432
Effective search space:   258336
Effective search space used:   258336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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 (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