GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Marinobacter algicola DG893

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_007154189.1 MDG893_RS12690 phosphoenolpyruvate--protein phosphotransferase

Query= TCDB::Q9HY55
         (956 letters)



>NCBI__GCF_000170835.1:WP_007154189.1
          Length = 942

 Score =  865 bits (2236), Expect = 0.0
 Identities = 486/952 (51%), Positives = 609/952 (63%), Gaps = 12/952 (1%)

Query: 1   MLELDTRQIRMGQRAADKAEALRLLGAALVADGLAAPGYAEGLKAREAQGSTYLGQGIAI 60
           ML L    IR+G  A D   AL      L   G   P Y  G+ ARE Q ST LG GIAI
Sbjct: 1   MLTLTANDIRLGCTATDWQAALNQASQELQDAGRTTPDYHAGMLAREQQSSTVLGNGIAI 60

Query: 61  PHGTPDTRELVFSTGVRLLQFPEGVDWGDGQQVYLAIGIAAKSDEHLQLLQLLTRALGEA 120
           PHGTP++R+ V STG+R+LQFP GV W D   VY+ + IAA+SDEHL +L+ LTR L + 
Sbjct: 61  PHGTPESRDAVTSTGIRVLQFPGGVTWHDNATVYVLVAIAAQSDEHLDILRHLTRVLDKP 120

Query: 121 DLGPALSAAASAEEVLGLLQGAPQELALDAQLVGLGQNAEDLDELAWLGARLLKKAGCVE 180
            L   L+ A   E ++ LL   P     DAQ + LG N     ELA   A  L+  GCV+
Sbjct: 121 GLSQKLAEADDTEALVSLLSKEPVVPKCDAQTLCLGVNTRATSELAISAAARLQGLGCVD 180

Query: 181 NGFAAVLQQTEPLPLGDGLCWLHSEQLVKRPGLAFVTPAQPLQHQGQLVTGLFCLASLGE 240
             F   +    P+ LG G   +H      RP LA  TP +P       + G+FCLA  G+
Sbjct: 181 ASFMKEIVSQPPVSLGQGFWLVHHSVGSIRPALALATPKEPRDD----LAGVFCLAGPGD 236

Query: 241 AHQALLERLCDLLLEGRGAELVRATSSRSVLAALGGELPPDWPSARAVLANPHGLHARPA 300
             + LLER+ + L +    E     S  +VL+ L GE   +  S R  L N HGLHARPA
Sbjct: 237 DCRELLERIDNFLAQNIPLE---NQSVDTVLSRLSGE-QANAVSDRVCLLNTHGLHARPA 292

Query: 301 QALAQLAKGFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPA 360
           + L Q A+    +IR+RL D +   VSA SL++++ LGARRGQTL  SA    AE A+ A
Sbjct: 293 KQLVQEARQHKADIRIRLEDGDGNSVSATSLTRIIGLGARRGQTLIISATGDDAEQAVAA 352

Query: 361 LLAAVREGLGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQAIAASPGIASGPAHVQ 420
           +  A+ +GLGE V  L ++    A  E E    P PL   E L+A+AASPG+A  PA V 
Sbjct: 353 VCQAINDGLGETVSPLRQQQSQPAPAEPE----PEPLADDEPLKAVAASPGLALAPAFVM 408

Query: 421 VAQRFEFQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIREIFVTHREMLDDPEL 480
                ++         +  RL RA    D ++  L+ ++       I   H EML D +L
Sbjct: 409 RQPTLDYPATASDAGEQTSRLGRAIDEADGQLRTLIRQAEGGEAAPILSVHVEMLQDDDL 468

Query: 481 AEQVQLRLNRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLCGVEA 540
            +     +N G SAEA W   ++ +A  QEAL D LLAERAADLRD+GRRVLA LCGV  
Sbjct: 469 YQAALEAINEGASAEAGWWLAIDTAARAQEALADRLLAERAADLRDVGRRVLANLCGVAM 528

Query: 541 PREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALVGAGAA 600
           P  P++PY+LV D++GPSDVARLD QRV G++TARGGATSHSAI+ARALG+PA+VGAG  
Sbjct: 529 PTPPDEPYVLVADDLGPSDVARLDTQRVRGLITARGGATSHSAILARALGLPAVVGAGDR 588

Query: 601 VLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPARTRDGHA 660
           +L +  GT L++DGE G L   P  E+  +     D   + QA A   R EPA T DGH 
Sbjct: 589 ILTISSGTVLVVDGERGCLVPNPGAERRDRIDRRLDQLTRLQADAHECRNEPATTTDGHT 648

Query: 661 VEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDALDGRP 720
           ++VCANLG+TA    AV+ GA+G+GLLRTEF+FM +  APDL TQ  EYR   DAL+G P
Sbjct: 649 IDVCANLGNTAHTPDAVDRGADGIGLLRTEFIFMEHPDAPDLDTQVKEYRHAFDALNGLP 708

Query: 721 LVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLTLQRPQILETQLRALFRAAGERPLRV 780
           LVARTLDVGGDKPL YWP+PHE+NP+LGLRGIRL+L RP+ILETQ+RAL  AA  RPLR+
Sbjct: 709 LVARTLDVGGDKPLDYWPLPHEDNPFLGLRGIRLSLTRPEILETQVRALLTAADNRPLRI 768

Query: 781 MFPMVGSLDEWRQARDLALRLREEIPLADLQLGIMVEVPSAALLAPVLAREVDFFSVGTN 840
           MFPMV  L+E+R A+ +  R+R EIP   LQ+G+M+EVPS ALLA  LA EVDFFSVGTN
Sbjct: 769 MFPMVKDLEEFRAAKAIVERVRAEIPCQGLQVGVMIEVPSCALLAHTLAPEVDFFSVGTN 828

Query: 841 DLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVCGELAADPLALPL 900
           DLTQYTLAIDRGH  LSA++DGLHP+VLQLI MTV AAHA  +WVG+CGELA+DP A+P+
Sbjct: 829 DLTQYTLAIDRGHGQLSAESDGLHPSVLQLIRMTVEAAHAHQRWVGICGELASDPQAIPV 888

Query: 901 LVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVRALVE 952
           L+GL VDELSV++R + LVKA +R L    AR  A+ ALG A+AAEVR  +E
Sbjct: 889 LLGLDVDELSVTSRRVPLVKACIRGLSRENAREQAKLALGKATAAEVRDALE 940


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: 1822
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: 942
Length adjustment: 44
Effective length of query: 912
Effective length of database: 898
Effective search space:   818976
Effective search space used:   818976
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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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:

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:

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:

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:

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