GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glt 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4464 C4-dicarboxylate
           transport protein
          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.

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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 paper from 2022 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