GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfQ in Shewanella sp. ANA-3

Align Galactofuranose-binding protein YtfQ (characterized)
to candidate 7024899 Shewana3_2073 periplasmic binding protein/LacI transcriptional regulator (RefSeq)

Query= SwissProt::P39325
         (318 letters)



>FitnessBrowser__ANA3:7024899
          Length = 313

 Score =  357 bits (917), Expect = e-103
 Identities = 180/308 (58%), Positives = 231/308 (75%), Gaps = 2/308 (0%)

Query: 7   IVSAVSAAMSSMALAAPLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIADGQQKQE 66
           I++A+     S   A   TVGFSQVGSESGWR + +   K+EA++RGI LK AD QQKQE
Sbjct: 6   IITALGLWAVSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQE 65

Query: 67  NQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKDKSLYMTTV 126
           NQIKAVRSF+AQGVDAI IAPVV TGW+PVLKEAK A+IPV ++DR+I V D SL++T +
Sbjct: 66  NQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLFLTRI 125

Query: 127 TADNILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAIDRKKGFAEAIKNAPNIKIIRS 186
            +D   EG+ IG WL+ +  G  C++ ELQGTVGA+ AIDR  GF + I N PN KI+RS
Sbjct: 126 ASDFSEEGRKIGQWLMDKTQGN-CDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRS 184

Query: 187 QSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKPGKDILTGS 246
           Q+G+FTR+KGKEVME F+KA+ NG+ +C V++HND+M +GA+QAIKEAGLKPGKDIL  S
Sbjct: 185 QTGEFTRAKGKEVMEGFLKAQ-NGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVS 243

Query: 247 IDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKLTLTKSTLYLPDTA 306
           +DGVPD +KAM DG+ NA+VEL+P + GPAFDA++ Y K      KL  T   ++  +TA
Sbjct: 244 VDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVFTQETA 303

Query: 307 KEELEKKK 314
             E EK++
Sbjct: 304 AAEYEKRR 311


Lambda     K      H
   0.313    0.130    0.363 

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: 334
Number of extensions: 8
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: 318
Length of database: 313
Length adjustment: 27
Effective length of query: 291
Effective length of database: 286
Effective search space:    83226
Effective search space used:    83226
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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