GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potE in Dyella japonica UNC79MFTsu3.2

Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate N515DRAFT_1063 N515DRAFT_1063 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= SwissProt::P0AAF1
         (439 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1063
          Length = 434

 Score =  213 bits (542), Expect = 1e-59
 Identities = 134/418 (32%), Positives = 208/418 (49%), Gaps = 8/418 (1%)

Query: 9   MGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFAKCGMFSRK 68
           +G   LT L + NM+GSG+ +LP  LA  G  S++ W  T  G++ LA   A        
Sbjct: 8   LGPWMLTALVVGNMIGSGVFVLPAALAPYGAASLLGWAFTMGGALLLALVHAWLAQLVAN 67

Query: 69  SGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVG-YGTELLGASLSPVQIGLA 127
            GG   YA  AFG +  F+A ++Y   +  AN AIA++  G  G     A+ +P +   A
Sbjct: 68  HGGAYAYARQAFGDTAGFVAAWSYWTCVWTANAAIAVAFAGSLGAIWPAANATPWRGTAA 127

Query: 128 TIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDSWNPHHAP 187
            + VLW+CT  N  G R  G++  +T    +IP++   + G        Y   +NP    
Sbjct: 128 ALAVLWLCTAINAAGVREAGRMQLVTTALKVIPLLVFGVCGLALVHGAAY-QPFNPSGQS 186

Query: 188 FFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIVSTNVIAG 247
             S   ++ A+TLWAFLGLE+A   T VV +P+R VP A + G L A V  +++   + G
Sbjct: 187 LPSVTTATAALTLWAFLGLEAATVPTGVVRDPQRTVPRATVAGMLVAGVATMLACTAVIG 246

Query: 248 IVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVFKSSSDEG 307
           ++P+     S AP   A AQ + P  G  +  +  +SC G+L GW     Q   +++ +G
Sbjct: 247 LLPHGAAQGSAAPMAAAAAQTWGPAAGWAMGLVATVSCLGALNGWVLLQGQTPYAAAQDG 306

Query: 308 YFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTNIIPYILS 367
            FP  F+R      P  G+L   ++ S L     S SL + F + + L+    ++PY+LS
Sbjct: 307 LFPAPFARTDARGTPWFGLLLSSVLASVLIAANGSKSLVALFTLSILLSTAATLLPYVLS 366

Query: 368 MAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFLGWTLY 425
           + A   I + A V    A      A +   YS +AL  +G EA+L+G ++  LG  ++
Sbjct: 367 VLAWWRIDRGAGVARRTA------AALALAYSLWALIGTGAEALLWGGVLLLLGLPVF 418


Lambda     K      H
   0.323    0.136    0.411 

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: 589
Number of extensions: 34
Number of successful extensions: 5
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: 439
Length of database: 434
Length adjustment: 32
Effective length of query: 407
Effective length of database: 402
Effective search space:   163614
Effective search space used:   163614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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