Alignments for a candidate for fruI in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Rhodococcus qingshengii djl-6-2

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_050655799.1 C1M55_RS13985 PTS transporter subunit EIIA

Query= TCDB::Q1LZ59
         (655 letters)



>NCBI__GCF_002893965.1:WP_050655799.1
          Length = 689

 Score =  389 bits (1000), Expect = e-112
 Identities = 248/681 (36%), Positives = 375/681 (55%), Gaps = 70/681 (10%)

Query: 5   DLLNKDVMLLDLQ-ATTKEAAIDEMVSKLVEQGIVTDFDTFKAGIMNREVQTSTGLGDGI 63
           ++++ +++ LD    +TKE  I  + ++L   G  +D        + RE Q++TGL  GI
Sbjct: 13  EIISPELISLDTDLGSTKEDVIRSLAARLTAAGRASDAAGLVDAALAREAQSATGLPGGI 72

Query: 64  AMPHSKNKAVKEATVLFAKSNKGVDYEALDGEPVDLFFMIAAPDGANDTHLAALAELSQY 123
           A+PH + +AV  A++ FA+ +  VD+ A DG P DL F+IAAP+GA   H+  L+ L++ 
Sbjct: 73  AIPHCRAEAVSSASLGFARLDPKVDFGAPDG-PADLVFLIAAPEGAGAEHMKLLSSLARA 131

Query: 124 LLKDGFADKLRQVTNPDDVINLFN-----------------------ATEEEKKEATPAA 160
           L++  F   LR+ + PD+++ L +                       +T +   E TPA 
Sbjct: 132 LVRPAFVTSLREASTPDEIVRLVDEVLNPAPKDPAAKAAAATPPAPVSTGKHATEETPAP 191

Query: 161 PVADSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIK 220
             A+ H  +VAVTAC TGIAHTYMA ++L       GV + VET G+SG    L    I 
Sbjct: 192 APAERH--IVAVTACPTGIAHTYMAADSLVAAGERAGVKVHVETQGSSG-STPLDPSVIA 248

Query: 221 RAKGVIIAADKAVE-MDRFNGKPLISRPVAEGIKKPEELINIILDGKAE--AYVADNSDL 277
            A  VI A D  V+  +RF GKP+++  V   I +P++++   L       A   D +  
Sbjct: 249 GAAAVIFATDVGVKGRERFAGKPVVASGVKRAINEPDKMLAEALRASENPAAATVDGTAA 308

Query: 278 SSEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLID--QFMGVPK-----S 330
           ++  S +   G G+   + L++GVS M+PFV  GG++IAL FL+   +  G  K     +
Sbjct: 309 AAADSDAGSVGFGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAKDIVLNN 368

Query: 331 SLSHL---GNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTG 387
           S+++L   G    + A+  Q+G+ AF F++P  A YIA++IA++PG+  GF AG++A   
Sbjct: 369 SITNLPDGGLATYLGAVLFQIGSLAFSFLVPALAGYIAFAIADRPGIAPGFTAGAVAVF- 427

Query: 388 LAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKS 447
                                 + +GF+G L GG +AG V L + +    VP+ L G+  
Sbjct: 428 ----------------------VGAGFIGGLVGGLIAGVVALYIGRIA--VPQWLRGLMP 463

Query: 448 ILLYPLLGVLVTGFLMLFV-NIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGG 506
           +++ PL   LV G LM  V   P+AAI + L ++L  LSG SA+ LG+I+G MM  D+GG
Sbjct: 464 VVIIPLFATLVVGALMFIVLGRPLAAITSGLTDWLNGLSGSSAIFLGIILGLMMCFDLGG 523

Query: 507 PFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNK-FTQEEHDA 565
           P NKAAY F  + L     A     +MA+VMA GMVPPLA+ +A+ + + K F++ E + 
Sbjct: 524 PVNKAAYAFAVAGLNVNDPAT--LRIMAAVMAAGMVPPLAMALASTVLRPKLFSEAEREN 581

Query: 566 GLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIA 625
           G    ++G +FI+EGAIPF A DP R IPS + G AVTGAL+    + L APHGGIFV  
Sbjct: 582 GKAAWLLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFF 641

Query: 626 LTSNPLLYLLYIAVGAVIAGI 646
                  +L+ +A G V+A +
Sbjct: 642 AVGGIGWFLVSLAAGTVVAAL 662


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: 1135
Number of extensions: 65
Number of successful extensions: 9
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: 655
Length of database: 689
Length adjustment: 39
Effective length of query: 616
Effective length of database: 650
Effective search space:   400400
Effective search space used:   400400
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources