GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glt in Pseudomonas fluorescens FW300-N2E3

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate AO353_02800 AO353_02800 C4-dicarboxylate transporter

Query= CharProtDB::CH_014038
         (428 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_02800 AO353_02800
           C4-dicarboxylate transporter
          Length = 444

 Score =  617 bits (1590), Expect = 0.0
 Identities = 306/410 (74%), Positives = 366/410 (89%)

Query: 5   LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64
           L+KSLYFQV+ AIAIGI LGH+YP+    +KPLGDGF+KLIKM+IAP+IFCTVV+GIAGM
Sbjct: 7   LYKSLYFQVIIAIAIGIALGHYYPQTAVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGM 66

Query: 65  ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124
           ++MK+VG+TG  ALLYFEIVSTIAL++GL++VN+VQPG GM++D +TLDA  VA Y    
Sbjct: 67  QNMKSVGKTGGYALLYFEIVSTIALLVGLVVVNIVQPGNGMHIDVSTLDASKVAAYVAAG 126

Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184
            DQ +V F++++IPA+++GAFA+G+ILQVL+F+V+FGFALHRLG+ G+ I + I+ F+ V
Sbjct: 127 ADQSVVGFLLNIIPATIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPILDFIDRFAHV 186

Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244
           +F IINMIM+LAPIGA GAMAFTIG YGVG+LVQLGQL+ CFYITC++F+++VLG IA+A
Sbjct: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMACFYITCVVFILVVLGGIARA 246

Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304
            GFS+ K IRYIREELLIVLGTSSSES LPRML KME+LG +KSVVGLVIPTGYSFNLDG
Sbjct: 247 HGFSVLKVIRYIREELLIVLGTSSSESVLPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306

Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364
           T+IYLTMAAVFIAQAT++ MDI HQITLL+VLLLSSKGAAGVTGSGFIVLAATLSAVGHL
Sbjct: 307 TAIYLTMAAVFIAQATDTHMDITHQITLLVVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366

Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVL 414
           PVAGLALILGIDRFMSEARALTNLVGN VAT+VVAKWVKELD  ++ + L
Sbjct: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELDVDQMHEEL 416


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: 690
Number of extensions: 23
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: 444
Length adjustment: 32
Effective length of query: 396
Effective length of database: 412
Effective search space:   163152
Effective search space used:   163152
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