GapMind for catabolism of small carbon sources

 

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

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Pf1N1B4_3487 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate

Query= TCDB::Q848I3
         (444 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3487 Aerobic
           C4-dicarboxylate transporter for fumarate, L-malate,
           D-malate, succunate, aspartate
          Length = 444

 Score =  804 bits (2076), Expect = 0.0
 Identities = 416/444 (93%), Positives = 431/444 (97%)

Query: 1   MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV 60
           MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV
Sbjct: 1   MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV 60

Query: 61  SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVA 120
           SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPG GMHIDV+TLD SK+A
Sbjct: 61  SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGAGMHIDVTTLDTSKIA 120

Query: 121 AYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFI 180
            +++AGKDQSI+GFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFI
Sbjct: 121 GFISAGKDQSIIGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFI 180

Query: 181 DRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVL 240
           DRFAHVMFNIINMIMKLAP+GA GAMAFTIGAYGVGSLVQLGQLMICFYITC+LFV++VL
Sbjct: 181 DRFAHVMFNIINMIMKLAPVGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCILFVVLVL 240

Query: 241 GAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300
           GAICRAHGFSV+KLIRYIREELLIVLGTSSSESALPRMLIKMERLGA+KSVVGLVIPTGY
Sbjct: 241 GAICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAQKSVVGLVIPTGY 300

Query: 301 SFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360
           SFNLDGTSIYLTMAAVFIAQATDT MD+T QITLLLVLLLSSKGAAGVTGSGFIVLAATL
Sbjct: 301 SFNLDGTSIYLTMAAVFIAQATDTPMDLTAQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360

Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGG 420
           SAVG LPVAGLALILGIDRFMSEARALTNLVGNAVAT+VVAKWVKELDED LQ ELASGG
Sbjct: 361 SAVGSLPVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELDEDTLQVELASGG 420

Query: 421 RAISDTREEDDLGVAEGPTPTTVK 444
           R ISD RE DDLGVAEGPTP +VK
Sbjct: 421 RGISDEREVDDLGVAEGPTPASVK 444


Lambda     K      H
   0.326    0.142    0.402 

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: 811
Number of extensions: 27
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: 444
Length of database: 444
Length adjustment: 32
Effective length of query: 412
Effective length of database: 412
Effective search space:   169744
Effective search space used:   169744
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 (21.6 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