GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Marinobacter adhaerens HP15

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component

Query= TCDB::Q1LZ59
         (655 letters)



>lcl|FitnessBrowser__Marino:GFF3783 HP15_3725 PTS system,
           fructose-specific IIBC component
          Length = 587

 Score =  335 bits (858), Expect = 5e-96
 Identities = 209/488 (42%), Positives = 284/488 (58%), Gaps = 44/488 (9%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228
           +VAVTAC TG+AHT+MA EAL   A   G  I+VET G+ G  + LT ++I  A  VI+A
Sbjct: 129 IVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVILA 188

Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAG 288
            D  V+  RF+GK +        +KKP + I   L+ +A    A     S  + S EK G
Sbjct: 189 CDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALE-QAVVLNAGQKKTSGASGSGEKKG 247

Query: 289 LGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQV 348
                YKHL++GVS MLP V+ GG++IALSF+        + +L+        AA+    
Sbjct: 248 P----YKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQEEGTLA--------AALMQIG 295

Query: 349 GNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLT 408
           G  AF  MIP+ A YIA+SIA++PGL  G + G +A              GE        
Sbjct: 296 GGTAFKLMIPLLAGYIAWSIADRPGLAPGMIGGFLA--------------GE-------- 333

Query: 409 GIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-N 467
            + +GFLG +  GFLAG V   + + L  +P S+E +K IL+ PLL  LVTG  M++V  
Sbjct: 334 -LGAGFLGGIVAGFLAGYVARFISQKLP-MPESIESLKPILIIPLLASLVTGLGMIYVIG 391

Query: 468 IPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAK 527
            PMAAI  AL  FL  +   +A+LLG I+G MM  D+GGP NKAAY FG   L+  +   
Sbjct: 392 EPMAAIMGALTGFLEGMGTTNAILLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGS--- 448

Query: 528 GGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAG 587
           GGS  MA++MA GMVP + + VA+ + + KF + E  AG  + V+GL FI+EGAIPF A 
Sbjct: 449 GGSAPMAAIMAAGMVPAIGMGVASFIARRKFAEAERQAGRASFVLGLCFISEGAIPFMAK 508

Query: 588 DPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIA 644
           DP R IP  ++G A+TGAL  L  +KLMAPHGG+FV+A+    S  L YL+ IAVG+++ 
Sbjct: 509 DPLRVIPVCMIGGAITGALSMLFTVKLMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVI 568

Query: 645 GILFGSLR 652
           G  +  L+
Sbjct: 569 GFGYALLK 576



 Score = 54.7 bits (130), Expect = 1e-11
 Identities = 38/120 (31%), Positives = 60/120 (50%), Gaps = 4/120 (3%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASG-VGNKLTADDIKRAKGVII 227
           L+ VTAC  G+A  ++A  AL++ A   G  +  +T G  G   NK +   I++A  VI 
Sbjct: 3   LIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLVIA 62

Query: 228 AADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKA 287
           A    V +D + GK L+  PV   +  P+    I+   +AEA   D +  S E+ ++  A
Sbjct: 63  AVGIPVNLDVYAGKRLLQIPVTAALPDPDA---ILTRAQAEATPWDPAMASQESIATSTA 119


Lambda     K      H
   0.320    0.137    0.381 

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: 949
Number of extensions: 54
Number of successful extensions: 11
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: 655
Length of database: 587
Length adjustment: 37
Effective length of query: 618
Effective length of database: 550
Effective search space:   339900
Effective search space used:   339900
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: 53 (25.0 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