GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3487
          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:

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