GapMind for catabolism of small carbon sources

 

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

Align Amino-acid permease RocE (characterized)
to candidate AO353_24825 AO353_24825 amino acid transporter

Query= SwissProt::P39137
         (467 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24825
          Length = 470

 Score =  537 bits (1383), Expect = e-157
 Identities = 246/452 (54%), Positives = 344/452 (76%)

Query: 8   GNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCL 67
           G  L R +KSRH+FM+SLGGVIGTG F+G+G TINQ GP+GA+L+YL+ GF+M+L M+CL
Sbjct: 9   GIHLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLIAGFLMYLVMVCL 68

Query: 68  GELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHID 127
           GEL+V  PVSGSFQT+ATKFI PA GF  GW+YW+ WA T  +EF +AG LM RWFP + 
Sbjct: 69  GELSVQMPVSGSFQTHATKFIGPATGFMIGWVYWMSWASTVGLEFTAAGMLMVRWFPTVP 128

Query: 128 VWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQ 187
           +W W  +F  ++F LNA+ T+AF E+E+WFSGIK+  IL FI++G   +FG I L  G  
Sbjct: 129 IWYWSALFVVVLFGLNALATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGAIPLTSGAP 188

Query: 188 APFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVW 247
           AP +++   D LFPNG+ A+   M+TV +AFQG E++GVAAGE++ PEK+IPR+++  V+
Sbjct: 189 APMMSNLIGDSLFPNGLPAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVF 248

Query: 248 RTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSG 307
           R L+F+VL+I+V++ ++PW+QAG++ESPFV VF+ +GIPYAAD+MNFVIL A+LSV NSG
Sbjct: 249 RVLIFYVLAIVVLSAIVPWQQAGLMESPFVQVFDMVGIPYAADLMNFVILTAILSVGNSG 308

Query: 308 LYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLL 367
           LYASTRIL+AM+  G A K+L   ++RGVP+ +L +T+  A +SL+T F  A+T++MVL+
Sbjct: 309 LYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFIAADTLFMVLM 368

Query: 368 SLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISL 427
           +++GMS  V WI I+L+Q  FRR YIR+GGK+ DLK++ P +P+LP++ + L   + + L
Sbjct: 369 AVSGMSGTVTWIVIALAQYKFRRAYIRDGGKLSDLKYRAPWFPLLPILCIALCCSLFVFL 428

Query: 428 AFDPEQRIALYCGVPFMIICYIIYHVVIKKRQ 459
           A D  QR +LY G  FM +CY  Y ++ +KRQ
Sbjct: 429 AMDETQRPSLYWGFGFMALCYGAYFLIQRKRQ 460


Lambda     K      H
   0.329    0.142    0.438 

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: 645
Number of extensions: 28
Number of successful extensions: 1
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: 467
Length of database: 470
Length adjustment: 33
Effective length of query: 434
Effective length of database: 437
Effective search space:   189658
Effective search space used:   189658
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 (21.8 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