GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Marinobacter adhaerens HP15

Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components

Query= TCDB::Q9HY55
         (956 letters)



>FitnessBrowser__Marino:GFF3781
          Length = 978

 Score =  867 bits (2239), Expect = 0.0
 Identities = 480/953 (50%), Positives = 624/953 (65%), Gaps = 11/953 (1%)

Query: 1   MLELDTRQIRMGQRAADKAEALRLLGAALVADGLAAPGYAEGLKAREAQGSTYLGQGIAI 60
           ML L    +R+G  A+D  +AL+     L   G  +P Y  G+ ARE Q ST LG GIAI
Sbjct: 36  MLTLTANDVRLGATASDWQDALQQAARDLERAGRTSPEYLAGMNAREQQSSTVLGNGIAI 95

Query: 61  PHGTPDTRELVFSTGVRLLQFPEGVDWGDGQQVYLAIGIAAKSDEHLQLLQLLTRALGEA 120
           PHGTP++R+ V  TGVR+LQFPEGV W DG +V++ + IAA+SDEHL +L+ LTR L + 
Sbjct: 96  PHGTPESRDAVLETGVRILQFPEGVSWHDGARVHVLVAIAAQSDEHLDILRHLTRVLDKP 155

Query: 121 DLGPALSAAASAEEVLGLLQGAPQELALDAQLVGLGQNAEDLDELAWLGARLLKKAGCVE 180
            L   L  A  A E++ LL  AP     D++ + LG +A   +ELA + A  L+   CV+
Sbjct: 156 GLAEKLGHATDATELVALLSKAPAVAKCDSETLCLGIDASTPNELALIAAARLQSLRCVD 215

Query: 181 NGFAAVLQQTEPLPLGDGLCWLHSEQLVKRPGLAFVTPAQPLQHQGQLVTGLFCLASLGE 240
             F A +    P+ LG G    H     +RP L+  TP +        + G+FCLA  G+
Sbjct: 216 TDFLASIVGQPPVDLGQGFWLTHHTVGARRPTLSLATPKRATAE----LRGVFCLAGPGD 271

Query: 241 AHQALLERLCDLLLEGRGAELVRATSSRSVLAALGGELPPDWPSARAVLANPHGLHARPA 300
               LLER+   L    G E ++  S+ ++LA L GE   D  +A+  L N HGLHARPA
Sbjct: 272 ECHDLLERIDTFLA---GDEPIQGLSAEALLARLSGEAA-DAVTAKVTLLNTHGLHARPA 327

Query: 301 QALAQLAKGFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPA 360
           + L Q A+     IR+RL + E A VSA SL++++ LGARRGQTL  SA    A  A+ +
Sbjct: 328 KQLVQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLLSATGDDASQAIQS 387

Query: 361 LLAAVREGLGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQAIAASPGIASGPAHVQ 420
           L +A+  GLGE+V  L        V EAE+   PA L   + ++A+AASPG+A  PA V 
Sbjct: 388 LTSAIEGGLGEKVSPLRSADPQTKVPEAEQ--APA-LTDDQPVKAVAASPGLALAPAFVM 444

Query: 421 VAQRFEFQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIREIFVTHREMLDDPEL 480
                E+    E    + +RL +A  + D ++  L+ ++       I   H EML D +L
Sbjct: 445 RQPTLEYPQFAEDSEQQIQRLNQAVDSADGQLRTLIRQAEGGEAAPILSVHVEMLQDEDL 504

Query: 481 AEQVQLRLNRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLCGVEA 540
            +     +N G SAEA W + ++ +A  QEAL D LLAERAADLRD+GRRVL+ LCGV  
Sbjct: 505 YQATLEAINEGASAEAGWWKAIDTAARGQEALADRLLAERAADLRDVGRRVLSNLCGVAM 564

Query: 541 PREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALVGAGAA 600
           P  P+ PYILV D++GPSDVARLD  RV G++TARGGATSHSAI+ARALG+PA+VG G  
Sbjct: 565 PTPPDTPYILVADDLGPSDVARLDTTRVRGLVTARGGATSHSAILARALGLPAVVGTGER 624

Query: 601 VLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPARTRDGHA 660
           +L +  G+ L++DGE G L   P  E+ ++           QA A   R +PA T DGH 
Sbjct: 625 ILTILNGSDLVVDGERGCLVPNPGAERCEKIRRRLQQLDALQAEAHENRNQPATTVDGHT 684

Query: 661 VEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDALDGRP 720
           +EVCANLG+TA    AVE GA+GVGLLRTEF+FM +  APDLATQ  EY+   DAL+G P
Sbjct: 685 IEVCANLGNTAHTPDAVERGADGVGLLRTEFIFMAHPEAPDLATQVTEYQHAFDALNGLP 744

Query: 721 LVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLTLQRPQILETQLRALFRAAGERPLRV 780
           LVARTLDVGGDKPL YWP+P E+NP+LG+RGIRL+L RP ILETQ+RAL  AAG+RPLR+
Sbjct: 745 LVARTLDVGGDKPLDYWPLPQEDNPFLGMRGIRLSLTRPDILETQVRALLTAAGDRPLRI 804

Query: 781 MFPMVGSLDEWRQARDLALRLREEIPLADLQLGIMVEVPSAALLAPVLAREVDFFSVGTN 840
           MFPMV  L+E+R AR +  +++ E+  +++Q+G+M+EVPS ALLA  LA EVDFFS+GTN
Sbjct: 805 MFPMVKDLEEFRAARAIVTKVQSEVSASNVQVGVMIEVPSCALLASTLAPEVDFFSIGTN 864

Query: 841 DLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVCGELAADPLALPL 900
           DLTQYTLAIDRGH  LSA++DGLHP+VL+LI MTV AAHA  +WVGVCGELA+DP A+P+
Sbjct: 865 DLTQYTLAIDRGHGQLSAESDGLHPSVLRLIRMTVEAAHAHNRWVGVCGELASDPQAIPV 924

Query: 901 LVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVRALVEA 953
           LVGL VDELSV++R + LVKA +R L L  AR  A KAL LA+A+EVR  +EA
Sbjct: 925 LVGLDVDELSVTSRRVPLVKACIRGLNLENARQQAEKALSLATASEVRDALEA 977


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: 1809
Number of extensions: 76
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: 978
Length adjustment: 44
Effective length of query: 912
Effective length of database: 934
Effective search space:   851808
Effective search space used:   851808
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 17 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