GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas fluorescens FW300-N2E3

Align valine/tyrosine/tryptophan amino-acid permease (characterized)
to candidate AO353_18555 AO353_18555 aromatic amino acid transporter

Query= CharProtDB::CH_091631
         (619 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_18555
          Length = 473

 Score =  199 bits (507), Expect = 2e-55
 Identities = 129/430 (30%), Positives = 212/430 (49%), Gaps = 10/430 (2%)

Query: 83  ESQEKNNLTKSIKSRHLVMISLGTGIGTGLLVGNGQVLGTAGPAGLVLGYGIASIMLYCI 142
           ++     L + +K+RH+ +I+LG  IGTGL +G+  VL +AGP+ ++LGY I   + + I
Sbjct: 4   QNSHSGTLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAICGFIAFMI 62

Query: 143 IQAAGELGLCYAGLTGNYTRYPSILVDPSLGFAVSVVYTIQWLTVLPLQLVTAAMTVKYW 202
           ++  GE+ +    + G+++ +         GF       I ++ V   +L      V YW
Sbjct: 63  MRQLGEM-IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYW 121

Query: 203 -TSVNADIFVAVVFVFVIIINLFGSRGYAEAEFIFNSCKILMVIGFVILAIIINCGGAGD 261
              V      AV FV +  INL   + + EAEF F   K++ ++G + L   +   G G 
Sbjct: 122 WPDVPTWASAAVFFVMINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHGG 181

Query: 262 RRYIGAEYWHNPGPFAHGFKGVCTVFCYAAFSYGGIEVLLLSAAEQENPTKSIPNACKKV 321
            +   +  W + G F +G  G+        FS+GG+E+L  +AAE + P   IP A  +V
Sbjct: 182 PQASVSNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQV 241

Query: 322 VYRILLIYMLTTILVCFLVPYNSDELLGSSDSSGS--HASPFVIAVASHGVKVVPHFINA 379
           +YRIL+ Y+   +++  L P+  D LL S ++SG     SPFV   +  G K   H +N 
Sbjct: 242 IYRILIFYIGALVVLLSLTPW--DSLLVSLNASGDAYSGSPFVQVFSMLGSKTAAHILNF 299

Query: 380 VILISVISVANSSLYSGPRLLLSLAEQGVLPKCLAYVDRNGRPLLCFFVSLVFGCIGFVA 439
           V+L + +SV NS  Y   R+LL +AEQG  PK LA +D+ G P+     S     +  V 
Sbjct: 300 VVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKGLAKIDKRGVPVRSILASAAVTFVAVVM 359

Query: 440 TSDAEEQVFTWLLAISSLSQLFIWMSMSLSHIRFRDAMAKQGRSMNEVGYKAQTGYWGSW 499
                +     L+++   + +  W  +S SH +FR  M    R+     +KA    +G++
Sbjct: 360 NYLIPQHALELLMSLVVATLVINWAMISYSHFKFRQHM---NRTKQTPLFKALWYPYGNY 416

Query: 500 LAVLIAIFFL 509
           + +    F L
Sbjct: 417 ICLAFVAFIL 426


Lambda     K      H
   0.324    0.138    0.420 

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: 696
Number of extensions: 34
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: 619
Length of database: 473
Length adjustment: 35
Effective length of query: 584
Effective length of database: 438
Effective search space:   255792
Effective search space used:   255792
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: 40 (21.5 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