Alignments for a candidate for fruII-ABC in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Rhodococcus qingshengii djl-6-2

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_050655799.1 C1M55_RS13985 PTS transporter subunit EIIA

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_002893965.1:WP_050655799.1
          Length = 689

 Score = 1095 bits (2831), Expect = 0.0
 Identities = 578/703 (82%), Positives = 622/703 (88%), Gaps = 17/703 (2%)

Query: 1   MSHSTPDRDSGPQIISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALAR 60
           MS +T    SGP+IIS +LISLDTDLG++KEDVI +L+ RL  AGRA++A  L DAALAR
Sbjct: 1   MSDTTAAGSSGPEIISPELISLDTDLGSTKEDVIRSLAARLTAAGRASDAAGLVDAALAR 60

Query: 61  ESQSATGLPGGIAIPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAE 120
           E+QSATGLPGGIAIPHCR+EAV +ASLGFARL PKVDFGAPDGPADLVFLIAAPEGAGAE
Sbjct: 61  EAQSATGLPGGIAIPHCRAEAVSSASLGFARLDPKVDFGAPDGPADLVFLIAAPEGAGAE 120

Query: 121 HMKLLSSLARALVRPAFVGALRDAKTPAEIVTLVNDVLAPAP---AATPAAAAPAAAAAA 177
           HMKLLSSLARALVRPAFV +LR+A TP EIV LV++VL PAP   AA  AAA P A  + 
Sbjct: 121 HMKLLSSLARALVRPAFVTSLREASTPDEIVRLVDEVLNPAPKDPAAKAAAATPPAPVST 180

Query: 178 APAAAAAVPAPKPEPVAPEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGV 237
              A    PAP P               +HIVAVTACPTGIAHTYMAADSLVAAGERAGV
Sbjct: 181 GKHATEETPAPAP-------------AERHIVAVTACPTGIAHTYMAADSLVAAGERAGV 227

Query: 238 VVHVETQGSSGSTPLAPGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTM 297
            VHVETQGSSGSTPL P VIAGA+AVIFATDVGVKG+ERFAGKPVVASGVKRAINEPD M
Sbjct: 228 KVHVETQGSSGSTPLDPSVIAGAAAVIFATDVGVKGRERFAGKPVVASGVKRAINEPDKM 287

Query: 298 ITEALRAGMNPSAAIVDAGSAGSAADEPAGSIGWGTHLRQVLLTGVSYMIPFVAAGGLLI 357
           + EALRA  NP+AA VD G+A +AAD  AGS+G+GTHLRQVLLTGVSYMIPFVAAGGLLI
Sbjct: 288 LAEALRASENPAAATVD-GTAAAAADSDAGSVGFGTHLRQVLLTGVSYMIPFVAAGGLLI 346

Query: 358 ALGFLLGGYEISGPAEDIVLSNSLGQLPEGGLATYLGAVLFQLGSLAFSFLVPALAGYIA 417
           ALGFLLGGYEISGPA+DIVL+NS+  LP+GGLATYLGAVLFQ+GSLAFSFLVPALAGYIA
Sbjct: 347 ALGFLLGGYEISGPAKDIVLNNSITNLPDGGLATYLGAVLFQIGSLAFSFLVPALAGYIA 406

Query: 418 FAIADRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVI 477
           FAIADRPG+APGFTAGAVAVFVGAGFIGGLVGGLIAGVVAL+I RI VPQWLRGLMPVVI
Sbjct: 407 FAIADRPGIAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALYIGRIAVPQWLRGLMPVVI 466

Query: 478 IPLFATLIVGALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLGIILGLMMCFDLGGPVN 537
           IPLFATL+VGALMF+VLGRPLA+ITSGLT+WLNGLSGSS IFLGIILGLMMCFDLGGPVN
Sbjct: 467 IPLFATLVVGALMFIVLGRPLAAITSGLTDWLNGLSGSSAIFLGIILGLMMCFDLGGPVN 526

Query: 538 KAAYAFAVAGLNVNDPASLRIMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAW 597
           KAAYAFAVAGLNVNDPA+LRIMAAVMAAGMVPPLAMALASTVLRP LFSEAERENGKAAW
Sbjct: 527 KAAYAFAVAGLNVNDPATLRIMAAVMAAGMVPPLAMALASTVLRPKLFSEAERENGKAAW 586

Query: 598 LLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFAIGNL 657
           LLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFA+G +
Sbjct: 587 LLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFAVGGI 646

Query: 658 LWFLVALAAGVVVAALCVVGAKEFIKPGASDAELDPDVATVAA 700
            WFLV+LAAG VVAAL VVGAKEF + G SDAELDP++   AA
Sbjct: 647 GWFLVSLAAGTVVAALAVVGAKEFFRKGPSDAELDPEIVPAAA 689


Lambda     K      H
   0.320    0.136    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: 1567
Number of extensions: 67
Number of successful extensions: 3
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: 700
Length of database: 689
Length adjustment: 39
Effective length of query: 661
Effective length of database: 650
Effective search space:   429650
Effective search space used:   429650
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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