GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27270 AO356_27270 MFS
           transporter
          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 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