Alignments for a candidate for fruI in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Oceanisphaera arctica V1-41

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_104485039.1 UN63_RS01625 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HY55
         (956 letters)



>NCBI__GCF_002936955.1:WP_104485039.1
          Length = 949

 Score =  808 bits (2088), Expect = 0.0
 Identities = 465/957 (48%), Positives = 597/957 (62%), Gaps = 18/957 (1%)

Query: 1   MLELDTRQIRMGQRAADKAEALRLLGAALVADGLAAPGYAEGLKAREAQGSTYLGQGIAI 60
           M  L  + ++ G   ADKA  ++ L   L  DG  A GY  G+  REAQ STYLGQGIAI
Sbjct: 1   MFSLTAQDVKTGVPLADKAAVIQALADWLEQDGHVAAGYGAGMLTREAQNSTYLGQGIAI 60

Query: 61  PHGTPDTRELVFSTGVRLLQFPEGVDWGDGQQVYLAIGIAAKSDEHLQLLQLLTRALGEA 120
           PHGT + R L+ +TG++ +  P+GV WG G++ YL +GIAA SDEHL LL+ L R L   
Sbjct: 61  PHGTQECRHLIKNTGIKAMHLPDGVPWGGGERAYLVLGIAAGSDEHLDLLKQLARTLSRD 120

Query: 121 DLGPALSAAASAEEVLGLLQGAPQ-----ELALDAQLVGLGQNAEDLDELAWLGARLLKK 175
            L   + AA  ++EVL LLQG  +     +  L A  V +   A  L+ L    A L++ 
Sbjct: 121 GLFERVKAARQSQEVLQLLQGNAESATETKFVLSADRVAVKARAGTLELLVEQAATLMQL 180

Query: 176 AGCVENGFAAVLQQTEPLPLGDGLCWLHSEQLVKRPGLAFVTPAQPLQHQGQLVTGLFCL 235
               E+     LQQ+  + +G G  WL       +PG A +T A  + H+ Q V+GL  L
Sbjct: 181 NPTEESA----LQQSAGMYIGQGW-WLKQIPADDKPGAALLT-ASGITHRQQPVSGLLAL 234

Query: 236 ASLGEAHQALLERLCDLLLEGRGAELVRATSSRSVLAALG-GELPPDWPSARAVLANPHG 294
           A  G  H+ LL R+ D L  GRGAEL    S+ ++L  L  G +         V+ N HG
Sbjct: 235 AVRGSEHKTLLTRVADWLAAGRGAELAGQDSAEALLNVLKRGPVSLSSHQRTVVVRNTHG 294

Query: 295 LHARPAQALAQLAKGFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIA 354
           LHARP   L Q AK F  +I+V   D +   VSAKSL K++ LG + G  L F AE   A
Sbjct: 295 LHARPGAMLVQAAKNFDADIQVCNLDGDEHWVSAKSLMKMIGLGVKAGHQLVFRAEGPDA 354

Query: 355 EDALPALLAAVREGLGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQAIAASPGIAS 414
           E AL AL  AV  GLGE   A A E  P A  E  +   P  +     ++ +AASPGIA 
Sbjct: 355 EAALDALTEAVNGGLGEAFVAQATE--PQA--EEHDIHEPQGIDPNTLVRGVAASPGIAI 410

Query: 415 GPAHVQVAQRFEFQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIREIFVTHREM 474
           GP  V    RF++  +      E+++L  A      E+   + R +    R++   HRE+
Sbjct: 411 GPVFVDAPLRFDYPQQAGDTQAEQQKLSAAIEQASAELSATLRRLSDTQARDMMSMHREL 470

Query: 475 LDDPELAEQVQLRLNRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLAR 534
           L D  L + V  R+ +G+SA AAW   ++ +A +Q A  DALLAERAAD+RD+GRRV+A 
Sbjct: 471 LADSSLTQGVSCRIKQGQSAAAAWWSEIDSAADRQAASSDALLAERAADIRDIGRRVMAI 530

Query: 535 LCGVEAPREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPAL 594
           LC       PE PY+ +  ++GPS +  LD  RV G++T  GGA+SHSAI+AR+LGIPAL
Sbjct: 531 LCHSRMTPPPEHPYLWLAQDIGPSQLVNLDPSRVLGLVTVGGGASSHSAILARSLGIPAL 590

Query: 595 VGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARAD-AQRLEPA 653
           V AG AV+ L  GT  +L+G+ G L VAP    L+QA   R  R++ QA  D  +R + A
Sbjct: 591 VAAGGAVMALPSGTEAILNGDDGTLWVAPEAAMLEQARV-RQQREREQAEQDWMRRHDAA 649

Query: 654 RTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVL 713
            T DGH + V ANL DT  A   +E+GAEGVGLLRTEFVFM     PDL  Q A YR+  
Sbjct: 650 ITLDGHRIGVAANLADTGQAREVMEVGAEGVGLLRTEFVFMARHSEPDLDEQLAFYRQAF 709

Query: 714 DALDGRPLVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLTLQRPQILETQLRALFRAA 773
           DALDGRPLVARTLDVGGDKPLPYWP+P E+NP+LG+RGIRL +Q+P++L+TQLRAL  AA
Sbjct: 710 DALDGRPLVARTLDVGGDKPLPYWPVPKEDNPFLGVRGIRLCMQKPELLKTQLRALLMAA 769

Query: 774 GERPLRVMFPMVGSLDEWRQARDLALRLREEIPLADLQLGIMVEVPSAALLAPVLAREVD 833
           G+RPLR+MFPMV    EWR A+ L  +++ E+   D+Q+GIMVEVPS AL A V A EVD
Sbjct: 770 GDRPLRIMFPMVADWSEWRWAKALFDKIQSEVQATDVQVGIMVEVPSVALNAAVFAEEVD 829

Query: 834 FFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVCGELAA 893
           FFS+GTNDLTQYTLA+DRG+  L+  +DGL+PAVL+LI M V AAHA+GKWVGVCGELA+
Sbjct: 830 FFSIGTNDLTQYTLAMDRGNGGLARLSDGLNPAVLRLIKMVVDAAHAKGKWVGVCGELAS 889

Query: 894 DPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVRAL 950
           DP+ALPLL+GLGVDELSVS + + LVKA VRE  L + R LA +AL    A  VR L
Sbjct: 890 DPVALPLLLGLGVDELSVSLKRVTLVKAQVREWSLSSCRKLAEQALQAVDAPAVRQL 946


Lambda     K      H
   0.318    0.134    0.382 

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: 1755
Number of extensions: 64
Number of successful extensions: 4
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: 956
Length of database: 949
Length adjustment: 44
Effective length of query: 912
Effective length of database: 905
Effective search space:   825360
Effective search space used:   825360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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 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