GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Dinoroseobacter shibae DFL-12

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  308 bits (788), Expect = 4e-88
 Identities = 176/507 (34%), Positives = 291/507 (57%), Gaps = 16/507 (3%)

Query: 1   MTTDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYH 60
           M++D     +    ++K + GV ALD+VDF+++ GE + L GENG+GKSTLIK ++GV  
Sbjct: 1   MSSDHDTAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEP 60

Query: 61  ADRGTIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNL-FIGREPKRFGLLRR 119
           A  GT+ + GQ     N   +   G+  ++Q+ +L PN+SVA+N+ F  +   R  L + 
Sbjct: 61  ATAGTVQIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKF 120

Query: 120 KEMEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQ 179
           + +   A   +   G  +D+   +    VA +Q+VAICRA+   A+++I+DEPT +L  +
Sbjct: 121 RAVRDIARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEK 180

Query: 180 EVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVK 239
           EV  L  ++R L++ GV++IFV+H L +V +VS+++ VLRNG  V      E     L  
Sbjct: 181 EVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTY 240

Query: 240 MMLGR---ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLG 296
            M GR   E+    +    +TL+        +  GK G+ +    ++R GE++G+ GLLG
Sbjct: 241 HMTGRDVPEVPPSDVAAGAQTLMQ------VQGLGKAGSFSDISFDLRTGEVLGITGLLG 294

Query: 297 SGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVR 356
            GRT  A+ +FG+   D+G+ L+ G P  L  P  AS+  IG+ PEDR T+G+  + S+ 
Sbjct: 295 CGRTSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSIL 354

Query: 357 ENII---LALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLL 413
            N+    L      G+L      ++   A  ++R+L ++ P  E P++ LSGGNQQ+V L
Sbjct: 355 RNVAVGRLDAHTSGGFLDMTGLAKE---ASDWLRRLKVKAPDVEAPVQSLSGGNQQRVAL 411

Query: 414 SRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVI 473
           +RWL   P+ LIL+ P+ G+DVG+ A+I  +I  L  +G+ ++VIS +L EL+    RV+
Sbjct: 412 ARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVL 471

Query: 474 IMRDRKQVAEIPLAELSVPAIMNAIAA 500
           +MR+ + +  +    L+   + + +A+
Sbjct: 472 VMREGRIIDALEGTALTEDDLAHRLAS 498


Lambda     K      H
   0.321    0.138    0.391 

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: 521
Number of extensions: 24
Number of successful extensions: 8
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: 500
Length of database: 498
Length adjustment: 34
Effective length of query: 466
Effective length of database: 464
Effective search space:   216224
Effective search space used:   216224
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 (21.8 bits)
S2: 52 (24.6 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