Alignments for a candidate for fruI in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Maridesulfovibrio zosterae DSM 11974

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_027722883.1 H589_RS0115585 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>NCBI__GCF_000425265.1:WP_027722883.1
          Length = 823

 Score =  672 bits (1735), Expect = 0.0
 Identities = 373/827 (45%), Positives = 511/827 (61%), Gaps = 20/827 (2%)

Query: 20  LRLSASPAGKEEAIREAAQLLIAAGCIDSAYAASMLRREAVANTFLGHGVAIPHGMVEDR 79
           + L A  +GK EAI +  ++L+  G I+  Y  SM RREAVANTFLG+G++IPHG+ E+R
Sbjct: 9   VNLGAKASGKLEAIEQVGKILVREGFIEPEYIDSMKRREAVANTFLGNGISIPHGLPENR 68

Query: 80  GMVRRSGIAVLQVPGGIAWNPGQTAHLVVAIAAQSDAHIAVLRRLTRLMQDEARLTALFT 139
             + ++G+A+LQVP G+ WNPG+T H+VV IAA+SD HI +L  LT ++ DE   + L  
Sbjct: 69  DKILKTGVAILQVPEGVIWNPGETVHIVVGIAARSDEHIEILTNLTHVLDDEQTTSRLAI 128

Query: 140 VTDPAALAAAL-GEDAPVAAPATPGGDLAERFDWVVDYPT----GLHARPATAWVETARA 194
             DPA +   L GE   V+ PA P  D+++ FD  +D       GLHARPAT +V+ A+ 
Sbjct: 129 TKDPAEIVRVLSGESRSVSRPA-PTLDVSD-FDVSIDVTIMGEHGLHARPATFFVDIAKK 186

Query: 195 SAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVAALARMKATITRLTARE 254
             + IQV       + K+L +LL+LG+  G ++ + A+GDDA  ALA +K  +      E
Sbjct: 187 YDSEIQVEFDGRSGNGKSLASLLKLGISGGKTMRIHAKGDDASLALATLKEAVDEGLGEE 246

Query: 255 KADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVHVLPRAAVSVPDEPVPLIE 314
             +AA    +      GW P +    +PG  ASPGLA GPVH    + + V         
Sbjct: 247 SEEAAIPRIE-----HGWRPQDVKQTIPGCTASPGLATGPVHQYTHSRIVVEAIAKDPKH 301

Query: 315 GGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQAEILNDTDLVTLACQLMVEGHG 374
               L  A++  R NL+ L ++   + G   AAIF A    L+D +++     L+  G  
Sbjct: 302 ESSELAHAIAAARLNLRHLYNEVRAKSGEPRAAIFRAHEAFLDDPEILVETEALIRNGKS 361

Query: 375 VAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTPCI 434
             ++W Q ++     L   D+ +LAARA DLRDVG+RVL  +   ++    P  P  P I
Sbjct: 362 AGYAWRQVIDDRVHILEQHDDELLAARAMDLRDVGRRVLRHLAGVVQD--QPFTPSRPVI 419

Query: 435 LIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTP 494
           L+AEDL+PSDTA LD + ++G  T+ GGPTSH+AI+AR+LG+PA+VA G +++E+ + T 
Sbjct: 420 LLAEDLTPSDTAQLDPSLILGFCTSGGGPTSHSAIIARSLGIPAIVAAGPSILEIVDDTI 479

Query: 495 AILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNR 554
           AI+DG SG L+L P+ +DI  A A     E  + EE   R  PA T DG  +E+ AN+ R
Sbjct: 480 AIIDGDSGNLYLEPSPSDIETADAAKLELEELRNEEYRARYEPALTTDGERIEVVANIGR 539

Query: 555 PDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIG 614
             +   A++ G E VGLMRTEFLFLER   P E+EQ+++Y+ M+ AL G P+I+R LDIG
Sbjct: 540 VSEAENAVNAGGEGVGLMRTEFLFLERDTPPDEEEQFQSYKTMVEALNGLPIIIRTLDIG 599

Query: 615 GDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFP 674
           GDK V +L LP E+NPFLG RG RL L RPE    QLRA++RA+K       G + IMFP
Sbjct: 600 GDKAVAYLDLPPEDNPFLGERGIRLCLNRPEFFLVQLRAIFRASK------YGPIRIMFP 653

Query: 675 MITALGEVQALRAACERIRAELDAPAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLT 734
           MI  L E++A +   E+ R E+ A A+ +GIMVEVP+    A   A+ VDFFSIGTNDLT
Sbjct: 654 MIATLDELEAAKRLAEKARIEVGAEALEIGIMVEVPSVVSMAREFAQVVDFFSIGTNDLT 713

Query: 735 QYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTG 794
           QY +AIDR HP LAA+ADSLHPAVLR+I   V+ ++  G W GVCGG+AG+P GA +L G
Sbjct: 714 QYVMAIDRVHPTLAAKADSLHPAVLRMIDQVVKASDEAGIWTGVCGGLAGEPLGATILAG 773

Query: 795 LGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVRAL 841
           LGV+ELSM    I AVK R+R   +   ++ AQ+AL C     VRAL
Sbjct: 774 LGVKELSMVVPSIAAVKARIRSISMKQARELAQKALSCRDNKQVRAL 820


Lambda     K      H
   0.319    0.134    0.387 

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: 1542
Number of extensions: 65
Number of successful extensions: 6
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: 846
Length of database: 823
Length adjustment: 42
Effective length of query: 804
Effective length of database: 781
Effective search space:   627924
Effective search space used:   627924
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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 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