GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AGP1 in Pseudomonas fluorescens FW300-N1B4

Align general amino acid permease AGP1 (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP

Query= CharProtDB::CH_091105
         (633 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559
          Length = 473

 Score =  201 bits (512), Expect = 5e-56
 Identities = 132/432 (30%), Positives = 214/432 (49%), Gaps = 16/432 (3%)

Query: 113 SDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQAC 172
           S  LK+ ++ RH+ +IALG  IGTGL +G+   L  AGP+ +++GYAI G I + I++  
Sbjct: 8   SGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAICGFIAFMIMRQL 66

Query: 173 GEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTSV 232
           GEM +V   + G ++ +         GF   W   + ++ V   EL      I YW   +
Sbjct: 67  GEM-IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDI 125

Query: 233 NPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGFI 292
              V    F+VL+  IN+   + + EAEF+F   K++ + G   LG  + V G G     
Sbjct: 126 PTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDGGPQAS 185

Query: 293 GGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAAK 351
               W   G F NG        G+   +    F+FGG E +  T AE   P+  IP A  
Sbjct: 186 VTNLWEHGGFFPNG------VSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAIN 239

Query: 352 QMIYRILFLFLATIILLGFLVPYNSD-QLLGSTGGGTKASPYVIAVASHGVRVVPHFINA 410
           Q+IYRIL  ++  +++L  L P++S    L ++G     SP+V   +  G     H +N 
Sbjct: 240 QVIYRILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNF 299

Query: 411 VILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAFCA 470
           V+L + LS+ NS  Y ++R+ L ++EQG APK  S ID+ G P+ ++  SA   ++A   
Sbjct: 300 VVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLL 359

Query: 471 ASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAM-KVQGRSLGELGFKSQTGVWGS 529
                +     L+++   + +  W  I  SH +FR+ M K +   L    FK+    +G+
Sbjct: 360 NYLVPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPL----FKALWYPYGN 415

Query: 530 AYACIMMILILI 541
            Y C+  ++ ++
Sbjct: 416 -YVCLAFVVFIL 426


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: 693
Number of extensions: 33
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: 473
Length adjustment: 36
Effective length of query: 597
Effective length of database: 437
Effective search space:   260889
Effective search space used:   260889
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:

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