GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pseudomonas fluorescens FW300-N1B4

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Pf1N1B4_4464 C4-dicarboxylate transport protein

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4464
          Length = 439

 Score =  463 bits (1191), Expect = e-135
 Identities = 223/413 (53%), Positives = 312/413 (75%)

Query: 7   KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66
           KSLYFQ+L A+ +G+++GHF+ +    +KPLGD F+KLIKM+IAPV+FCT+VTGIAGM  
Sbjct: 9   KSLYFQILCAVLLGVVVGHFWAQQAIALKPLGDAFIKLIKMMIAPVVFCTIVTGIAGMND 68

Query: 67  MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126
            +++GR  +  +L F  ++ I+L IGL+ V V +PGAGMN+DP+ L    ++ Y + A  
Sbjct: 69  KRSLGRLLSKTMLLFLGLTVISLFIGLVAVYVFKPGAGMNIDPSHLSTAGLSQYTESAAK 128

Query: 127 QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIF 186
            G+V F M +IP + IGAF+ G +L VL  AVL GFAL  LG +G+ + +V+E+ SQ++F
Sbjct: 129 LGVVEFFMHIIPDTFIGAFSKGEVLPVLFIAVLCGFALSSLGDRGKPVLDVLEAASQMVF 188

Query: 187 GIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATG 246
            I + +MR APIGAFGA+AFT+G+YG+ +L  L +LI+  Y+ C  FV +VLGSI +A G
Sbjct: 189 KIFSYLMRFAPIGAFGALAFTVGQYGITSLGSLAKLIMTLYVACAFFVFVVLGSICRAHG 248

Query: 247 FSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTS 306
           FS++K +RY+REE L+VLGTSS+E  +PRML+K++ LGC K VVGLV+PTGYSFNLDGT+
Sbjct: 249 FSLWKLLRYLREEFLVVLGTSSTEPVMPRMLEKLQALGCSKGVVGLVLPTGYSFNLDGTA 308

Query: 307 IYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 366
           IYL++AA+FIAQA N  + +   +T+L ++LLSSKGAAGVTGSGF+ LA+TL+ +  +P+
Sbjct: 309 IYLSLAAIFIAQACNIDLTVTQTLTMLAIMLLSSKGAAGVTGSGFVALASTLTVIHDIPL 368

Query: 367 AGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAP 419
           AGLAL++GIDRFMSEARALT+L  N VAT+V++      D + L D L+ + P
Sbjct: 369 AGLALLIGIDRFMSEARALTSLASNAVATVVISISENACDRQVLLDTLDGKKP 421


Lambda     K      H
   0.327    0.142    0.401 

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: 532
Number of extensions: 20
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: 428
Length of database: 439
Length adjustment: 32
Effective length of query: 396
Effective length of database: 407
Effective search space:   161172
Effective search space used:   161172
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.

Links

Downloads

Related tools

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