GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Pseudomonas fluorescens FW300-N2C3

Align D-fructose transporter, sugar porter family (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter

Query= reanno::Korea:Ga0059261_1777
         (458 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27270
          Length = 472

 Score =  245 bits (625), Expect = 3e-69
 Identities = 148/432 (34%), Positives = 229/432 (53%), Gaps = 9/432 (2%)

Query: 29  AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88
           A  GGLLFGFDT VI+GA   ++   GLT    G   ++ LIG ++G+L +G  +D  GR
Sbjct: 35  ATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSDLKGR 94

Query: 89  KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148
           + ++L +A+ + + +L   LAP LN  +  RF  GLA+G ASVV P Y+AE++P+  RGR
Sbjct: 95  RRIILFLAVVFFLGALACALAPTLNVMVAARFTLGLAVGGASVVVPAYLAEMAPSSIRGR 154

Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLV-QYDVAWRWMFGIVAVPSTIFLLVTLLLPESPR 207
           ++  N+L IV G  +AF +N  +  L    D  WRWM  +  +P+    L  L +PESPR
Sbjct: 155 IITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMPESPR 214

Query: 208 WLAIHGQADRARDVMQRLG---FADPRAELARIELAEAREEAAGKPR-LFQRSHFTPVAC 263
           WLA  G+     +V++ +    +A    E    +++  R    G  R L Q+        
Sbjct: 215 WLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDLSQKGARRIFLI 274

Query: 264 AIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFG 323
            I IA+ +QL+G+N+++Y+  +I   AG    SAL+ ++  G  ++  T   + L+DR G
Sbjct: 275 GIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGVISIGATFVGIALLDRVG 334

Query: 324 RRPLLFVGSVICAATLLLVGWQLESAKPDGT---LILFGLLGFIAAFAMSQGAVIWVFIS 380
           RRP++ +G      +LLL+G       P  T   LIL  +  F+A+     G   WV ++
Sbjct: 335 RRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTRAMLILGAMAMFLASMQGLIGPAFWVLLA 394

Query: 381 EVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTWKF 439
           E+FP  +RG    +     W+    I   FP   A++G G  F  F    LL L +   +
Sbjct: 395 EIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVATIGIGQTFFVFVGAGLLSLTFVAVW 454

Query: 440 MPETNGIALEDM 451
           +PET G  LE++
Sbjct: 455 VPETRGSTLEEI 466


Lambda     K      H
   0.327    0.139    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: 588
Number of extensions: 36
Number of successful extensions: 6
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: 458
Length of database: 472
Length adjustment: 33
Effective length of query: 425
Effective length of database: 439
Effective search space:   186575
Effective search space used:   186575
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