GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Azospirillum brasilense Sp245

Align Inositol transport system ATP-binding protein (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  153 bits (387), Expect = 6e-42
 Identities = 91/243 (37%), Positives = 136/243 (55%), Gaps = 5/243 (2%)

Query: 4   SQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGD 63
           S PL+ ++G+ K F  V AL GV   V  GE H LLG+NGAGKST IKT++GV++   G 
Sbjct: 9   SPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGT 68

Query: 64  ILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDY 123
           +  EG+ +      +A    I TV+Q + ++P +SV+ N F+G +P+R      L D   
Sbjct: 69  VTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMR----FGLVDRGA 124

Query: 124 ANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183
             R     +   G+ L      +G  S   +Q VAIARAV   AKVLILDEPT++L  ++
Sbjct: 125 MRRRARAVLIPYGLTL-DVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQE 183

Query: 184 TANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243
            A +   +  +R +G+ +VF+TH +    A+ DR TVL  G+ +G  +  ++   +L  M
Sbjct: 184 VAVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAM 243

Query: 244 MAG 246
           M G
Sbjct: 244 MLG 246



 Score = 82.4 bits (202), Expect = 2e-20
 Identities = 56/238 (23%), Positives = 112/238 (47%), Gaps = 9/238 (3%)

Query: 6   PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65
           PL+R +G    +G   ++    +D+ PGE   L G  G+G++   + + G+ +  +G+  
Sbjct: 270 PLVRFRG----YGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAA 325

Query: 66  FEGQPLHFADPRDAIAAGIATVHQHL---AMIPLMSVSRNFFMGNEPIRKIGPLKLFDHD 122
            +GQ +    PRDAI  G     +      ++  +SV  N  +  +   + G L+     
Sbjct: 326 VDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQA--RQGWLRPIPRC 383

Query: 123 YANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVR 182
               I    +R + I     +Q +  LSGG +Q   +AR +    ++LILDEPT  + V 
Sbjct: 384 RQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVG 443

Query: 183 QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240
             A ++  I+++   G+A++ ++  +   +A   R  VL   + +   + G+++ + +
Sbjct: 444 AHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRI 501


Lambda     K      H
   0.321    0.137    0.395 

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: 343
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 516
Length adjustment: 30
Effective length of query: 231
Effective length of database: 486
Effective search space:   112266
Effective search space used:   112266
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 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