GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3607108 Dshi_0530 ABC transporter related
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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