Alignments for a candidate for fruII-ABC in Phaeacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Phaeacidiphilus oryzae TH49

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_051940990.1 BS73_RS28560 fructose-specific PTS transporter subunit EIIC

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_000744815.1:WP_051940990.1
          Length = 671

 Score =  622 bits (1604), Expect = 0.0
 Identities = 362/697 (51%), Positives = 450/697 (64%), Gaps = 51/697 (7%)

Query: 5   TPDRDSGPQIISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQS 64
           T D  +G  + +  L+ L    G +  D + AL++RLA AGR T+ +       AR+ Q+
Sbjct: 10  TADASAGATLTTPALVDLYLAPGDTP-DALRALAQRLAAAGRVTDLEGFLADIAARQEQA 68

Query: 65  ATGLPGGIAIPHCRSEAVVAASLGFARLAPKVDFGAPDG-PADLVFLIAAPEGAGAEHMK 123
            TG+  GI +PHCRS  V   SL F R    +DF APDG PADLVF+IAAP GA   H++
Sbjct: 69  PTGMGDGIGVPHCRSAHVTQPSLAFGRSVGGLDFDAPDGRPADLVFMIAAPAGADDAHLE 128

Query: 124 LLSSLARALVRPAFVGALRDAKTPAEIVTLVNDV--LAPAPAATPAAAAPAAAAAAAPAA 181
           +L++LAR LVR  F  ALR A  P  +  L+N     A  PAA P AAA A A AAAPAA
Sbjct: 129 ILAALARRLVREDFTRALRAATDPTAVAALLNSTGGAAVEPAAEPTAAAAAPAPAAAPAA 188

Query: 182 AAAVPAPKPEPVAPEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHV 241
            +A  A                    +VAVT+CPTGIAHTYMAA+ L  A  RAGV + V
Sbjct: 189 QSAPAATL-----------------RLVAVTSCPTGIAHTYMAAERLEQAAARAGVEIAV 231

Query: 242 ETQGSSGSTPLAPGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEA 301
           ETQGS+GSTPL P VIA A AV+ A DV ++ + RFAGKPVV  GVK A+N PD +I  A
Sbjct: 232 ETQGSAGSTPLDPAVIAAADAVVLAHDVEIRDRARFAGKPVVDVGVKAAVNRPDELIARA 291

Query: 302 LRAGMNPSAAIVDAGSAGSAADEPA-------GSIGWGTHLRQVLLTGVSYMIPFVAAGG 354
             +          AGSA +A D PA           W T LRQ L++GVSYMIPFVAAGG
Sbjct: 292 RES----------AGSAPAAGDRPAPEPRPVEAPPHWATRLRQYLMSGVSYMIPFVAAGG 341

Query: 355 LLIALGFLLGGYEISGPAEDIVLSNSLGQLPEGGLATYLGAVLFQLGSLAFSFLVPALAG 414
           LLIALGF +GGY+I   A  +V     G       +++  A+LFQ GS AF FLVP LAG
Sbjct: 342 LLIALGFAVGGYQIKS-APSVV-----GHFDWTASSSW-AALLFQAGSAAFGFLVPILAG 394

Query: 415 YIAFAIADRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMP 474
           +IA+AIADR  LA G   GAV+V VGAGF+GG+V GL+AGV+  W+ R  VP+ + G+MP
Sbjct: 395 FIAYAIADRAALAAGIVGGAVSVTVGAGFLGGIVAGLLAGVLVRWMVRWKVPKGVAGIMP 454

Query: 475 VVIIPLFATLIVGALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLGIILGLMMCFDLGG 534
           VV+IPL +  ++G LMF+VLG+P+A+  SGLT+WLNG+SG + + LG++LG MM FD+GG
Sbjct: 455 VVVIPLISVAVIGFLMFVVLGQPIATAMSGLTHWLNGMSGGNAVILGVVLGAMMAFDMGG 514

Query: 535 PVNKAAYAFAVAGLNV--NDP--ASLRIMAAVMAAGMVPPLAMALASTVLRPSLFSEAER 590
           P+NK AY FA   L    +DP   SL++MAAVMAAGM PPL +ALA TV+R  LFS  ER
Sbjct: 515 PLNKVAYTFAAGALTTAGSDPGAGSLKVMAAVMAAGMTPPLGLALA-TVVRRRLFSAEER 573

Query: 591 ENGKAAWLLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFV 650
           ENGKAAW+LG++FI+EGAIPFAAADPLRVIPS M G  V G L M F  TL APHGGI+V
Sbjct: 574 ENGKAAWVLGASFITEGAIPFAAADPLRVIPSGMLGSMVVGGLSMWFGATLRAPHGGIWV 633

Query: 651 FFAIGNLLWFLVALAAGVVVAALCVVGAKEFI-KPGA 686
              IG  L +++A+AAG  V A  V+  K     PGA
Sbjct: 634 LPLIGRPLLYVLAIAAGTAVTAAAVITLKSLRGTPGA 670


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: 1387
Number of extensions: 89
Number of successful extensions: 7
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: 671
Length adjustment: 39
Effective length of query: 661
Effective length of database: 632
Effective search space:   417752
Effective search space used:   417752
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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