Alignments for a candidate for fruI in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Halomonas desiderata SP1

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_086509381.1 BZY95_RS07800 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HY55
         (956 letters)



>NCBI__GCF_002151265.1:WP_086509381.1
          Length = 963

 Score =  933 bits (2412), Expect = 0.0
 Identities = 534/970 (55%), Positives = 650/970 (67%), Gaps = 25/970 (2%)

Query: 1   MLELDTRQIRMGQRAADKAEALRLLGAALVADGLAAPGYAEGLKAREAQGSTYLGQGIAI 60
           ML L    +R+  +A D  +AL     +L   GL AP Y +GL  REAQ STYLG  IAI
Sbjct: 1   MLTLRPEDVRLDCQAPDWRDALEQAAESLHRAGLTAPAYRDGLFQREAQSSTYLGNAIAI 60

Query: 61  PHGTPDTRELVFSTGVRLLQFPEGVDWGDGQQVYLAIGIAAKSDEHLQLLQLLTRALGEA 120
           PHGT ++RE V +TGVR+LQFP GV+W DGQ+V++ + IAA+SDEHL +L+ LT  L + 
Sbjct: 61  PHGTAESREHVLATGVRVLQFPAGVEWHDGQRVHVLVAIAAQSDEHLDILRQLTHVLDDD 120

Query: 121 DLGPALSAAASAEEVLGLLQGAPQELALDAQLVGLGQNAEDLDELAWLGARLLKKAGCVE 180
            +G  L+ A+SAE V  LL  A  E  LD   + LG  A D  ELA  GA  L++ GCV 
Sbjct: 121 RVGERLAGASSAETVAALLSKAQVEARLDTDTLCLGFPARDARELALAGAARLRQLGCVG 180

Query: 181 NGFAAVLQQTEPLPLGDGLCWLHSEQLVKRPGLAFVTPAQPLQHQGQLVTGLFCLASLGE 240
           +GF A + + E  PLG GL     E+ V  P LA  TP + L+  G+ V G+FCLA+ G+
Sbjct: 181 SGFVAEVAERELAPLGQGLWLSLGERSVTVPALALATPDERLESGGEAVKGVFCLAAQGD 240

Query: 241 AHQALLERLCDLLLEGRGAELVRATSSRSVLAALGGELPPDWPSARAVLANPHGLHARPA 300
           AH+ LLER+  LL  G  AEL  A ++ +VLA L GE          VL N HGLHARPA
Sbjct: 241 AHRGLLERVLTLLDSGAAAELPSADAA-TVLARLAGESAAAHTRLARVL-NAHGLHARPA 298

Query: 301 QALAQLAKGFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPA 360
           + L Q A+     I+VRLA+   A VSA SL+K++ LGARRGQ L FSAE   A+ AL A
Sbjct: 299 KQLVQAAREQGLPIQVRLAEGGGAAVSASSLTKVINLGARRGQQLLFSAEGEGAQQALDA 358

Query: 361 LLAAVREGLGEEV---EALAEEALPDAVGEAEEDARPA-PLRAGERLQAIAASPGIASGP 416
           +  AV +GLGE V   +   E ++P A      DA P  PL        +AASPG+A  P
Sbjct: 359 VCRAVADGLGEHVLPFDESRERSMPQA------DAAPVEPLPDDVPHPGVAASPGLAIAP 412

Query: 417 AHVQVAQRFEFQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIREIFVTHREMLD 476
           A V    RF++  R   PA ++ RL +A      ++  LV ++    + +I   H EML 
Sbjct: 413 AFVLQTPRFDYPERAADPAEQQRRLRQALAEGAAQLEALVRQARGGEVAQILSMHEEMLT 472

Query: 477 DPELAEQVQLRLNRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLC 536
           DPEL E  +  +  G SAE+AW   +E +A  QE L D LLAERAADLRD+GRRVL  LC
Sbjct: 473 DPELFEAAREGIQEGRSAESAWWEAIETAAHAQEMLADRLLAERAADLRDVGRRVLGVLC 532

Query: 537 GVEAPREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALVG 596
            V+ P  PE PYILV D++GPSDVARLD QRV G+LTARGGAT+HSAI+ARALGIPA+VG
Sbjct: 533 EVQLPEPPETPYILVTDDIGPSDVARLDTQRVRGLLTARGGATAHSAILARALGIPAVVG 592

Query: 597 AGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPARTR 656
           AG  VL L  G  L+LDGE G +  APS E+   A      R++R+A A   R  PA+TR
Sbjct: 593 AGERVLTLAGGQELILDGERGRVIPAPSAERRASAEQRLAERERREAEAWQARFAPAQTR 652

Query: 657 DGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDAL 716
           DGH VEV ANLG+TA AA AVE GAEG+GLLRTEF+FM +AR PDLATQ  EYR  LDAL
Sbjct: 653 DGHRVEVAANLGNTAHAADAVERGAEGIGLLRTEFLFMAHAREPDLATQIEEYREALDAL 712

Query: 717 DGRPLVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLTLQRPQILETQLRALFRAAG-- 774
           +GRPLVARTLDVGGDKPLPYWP+P E+NP+LGLRGIRL+L RP++LETQLRAL  AA   
Sbjct: 713 EGRPLVARTLDVGGDKPLPYWPVPKEDNPFLGLRGIRLSLTRPEVLETQLRALLMAAAPA 772

Query: 775 -------ERPLRVMFPMVGSLDEWRQARDLALRLREEIPLA----DLQLGIMVEVPSAAL 823
                   RPLR+M PMV  + E+R  R +  RL +EIP A    D+QLG+M+EVPSAAL
Sbjct: 773 ASEAADKPRPLRIMLPMVKDVGEFRATRAIFERLLDEIPAAERATDVQLGVMIEVPSAAL 832

Query: 824 LAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGK 883
           LA  LA EVDFFSVGTNDLTQYTLAIDR HP LSAQADGLHPAVL+LI+MTV AAHA GK
Sbjct: 833 LASALAAEVDFFSVGTNDLTQYTLAIDRDHPELSAQADGLHPAVLRLIEMTVAAAHAHGK 892

Query: 884 WVGVCGELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLAS 943
           WVGVCGELA+D LA+P+LVGLGVDELSVSAR + LVKA +RE  L  AR  A+ AL  A+
Sbjct: 893 WVGVCGELASDTLAVPVLVGLGVDELSVSARQVPLVKARLREFDLAEARAQAQLALAQAT 952

Query: 944 AAEVRALVEA 953
           +  VR  +EA
Sbjct: 953 SEAVRDALEA 962


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: 2000
Number of extensions: 79
Number of successful extensions: 5
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: 963
Length adjustment: 44
Effective length of query: 912
Effective length of database: 919
Effective search space:   838128
Effective search space used:   838128
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