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_4413 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4413
          Length = 451

 Score =  489 bits (1258), Expect = e-143
 Identities = 240/438 (54%), Positives = 327/438 (74%), Gaps = 2/438 (0%)

Query: 7   LYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGM 66
           ++  LY QV++A+ +G ++G F P+TG ALKPLGD FIKLIKM++AP+IF TVV+GIA M
Sbjct: 4   IFGKLYVQVLIAVILGAIVGVFVPETGTALKPLGDAFIKLIKMLLAPVIFLTVVTGIARM 63

Query: 67  QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAG 126
           +NMK +G+ G  AL+YFE+VST+AL++GLVVV+V +PG GM+IDV++LD S +A Y TA 
Sbjct: 64  ENMKELGRVGFRALIYFEVVSTLALVVGLVVVDVFKPGAGMNIDVASLDTSSLATYTTAV 123

Query: 127 KDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHV 186
           K  S + F++N+IP+TIV AFA G++LQ+L+FS++ G AL  +G   K  +D +D     
Sbjct: 124 KHASFMDFVMNIIPDTIVDAFAKGNVLQILLFSILLGVALAHVGPRAKVFVDTLDSLMQG 183

Query: 187 MFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRA 246
           MF I+NM+M+LAPIGA GA+AFTIG YG GSL  LG+LM C Y+TC +FV+ VLG ICR 
Sbjct: 184 MFRIVNMVMRLAPIGAFGAIAFTIGKYGFGSLFSLGKLMACVYLTCAVFVIFVLGPICRY 243

Query: 247 HGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306
            GFS+ K +++I+EEL  VLGTSSSES LP+M+ KME+ G  K V G++IP+G +FN DG
Sbjct: 244 SGFSLWKFLKFIKEELFTVLGTSSSESVLPQMISKMEKAGVSKPVAGMIIPSGLTFNPDG 303

Query: 307 TSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366
            +IY T+AA+FIAQAT+T + +T Q+ +L VL+ +SKG+AGVTGSGFI+LAATLS++G +
Sbjct: 304 QAIYYTIAAIFIAQATNTPLTLTDQLIVLAVLMFTSKGSAGVTGSGFIILAATLSSLGTI 363

Query: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGGRAISDT 426
           PVAG+ L+LG+DRFMSEARA+TN +GN V T+ +AKWV  LD  ++   L   G A    
Sbjct: 364 PVAGMVLLLGVDRFMSEARAITNTIGNGVGTMAIAKWVGALDTVKMHKAL--NGEAAEQK 421

Query: 427 REEDDLGVAEGPTPTTVK 444
            E     +   P+    K
Sbjct: 422 PETVQADIVAVPSAMPAK 439


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: 612
Number of extensions: 21
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: 451
Length adjustment: 33
Effective length of query: 411
Effective length of database: 418
Effective search space:   171798
Effective search space used:   171798
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.

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