GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Magnetospirillum magneticum AMB-1

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_011386738.1 AMB_RS22220 phosphoenolpyruvate--protein phosphotransferase

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



>lcl|NCBI__GCF_000009985.1:WP_011386738.1 AMB_RS22220
           phosphoenolpyruvate--protein phosphotransferase
          Length = 596

 Score =  340 bits (872), Expect = 1e-97
 Identities = 213/577 (36%), Positives = 322/577 (55%), Gaps = 25/577 (4%)

Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVP---LIEGGDRLHEALSLTRQNLKALADDTAR 339
           G+  S G+AIG +++     ++VP+  +P   L     R +EA +   + ++ L D   R
Sbjct: 25  GLGVSRGIAIGTLYLHDAGTITVPELRIPAARLDAECARFNEASANAGRQVEQLQDKAGR 84

Query: 340 ---RLGPSEAAIFAAQAEILNDTDLVT-LACQLMVEGHGVAWSWHQAVERTAAGLAALDN 395
                G     +  A  ++L+ + L+  +  ++  +      +  Q +     G  A+++
Sbjct: 85  LGGAAGEELGYLLDAYRQMLHGSRLLRGVEARIRNDRINAEAAVQQEINEIVRGFEAMED 144

Query: 396 PVLAARAADLRDVGQRVL-ARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVI 454
           P LAAR AD++D+G+R+L A  + A R   A  LP    +++AE+++P+DTA LD  +V 
Sbjct: 145 PYLAARVADIKDIGRRLLRALTNTAYRPFTA--LPRN-AVIVAEEMTPADTALLDPNQVA 201

Query: 455 GLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIA 514
           GLAT  GG   HTAI+AR+LGLP+++     L  +  G   I+DG +G + ++P    +A
Sbjct: 202 GLATVMGGSEGHTAIMARSLGLPSVLGIADLLTGVKGGEQVIIDGTNGLVVINPGPETLA 261

Query: 515 DARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRT 574
             R   A     +      + +PA TRDG  + + AN+  P++V   L  GAE +GL+R+
Sbjct: 262 FYRRERAAFLKARRVLSRLKDVPAVTRDGGRITLQANMELPNEVGAVLDSGAEGIGLLRS 321

Query: 575 EFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGV 634
           EFL++ R D P EDEQY   + ++  + GR + VR  D GGDK  P L      NP LG+
Sbjct: 322 EFLYMNRDDVPSEDEQYAILKDVVERMGGRTVTVRTFDAGGDKLAPALGCTIGPNPSLGL 381

Query: 635 RGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERI-- 692
           R  RL L R +LLE QL A+ RA+  G  +      I+ PMI  +GE++A R    R+  
Sbjct: 382 RAIRLGLARQDLLEAQLAAILRASAHGPVR------ILIPMIATVGELRATREVMNRVIR 435

Query: 693 -----RAELDAPAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPEL 747
                   L  P   LG M+E+P AA+ AD +A H DFF+IGTNDL QY LAIDR    +
Sbjct: 436 RLRKAGVSLPDPLPRLGAMIEIPGAALSADSIAWHADFFAIGTNDLVQYTLAIDRSDEAV 495

Query: 748 AAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDI 807
           A   + LHPAVLRLI+ T + A+R    V VCG +AGDP  A LL GLG+R+LSM+  ++
Sbjct: 496 AHLYNPLHPAVLRLIQFTTQAAQRANIPVSVCGEMAGDPRYAPLLLGLGLRDLSMSTSNL 555

Query: 808 PAVKDRLRGSDLSALKDAAQRALD-CETADAVRALDG 843
           P VK+R+R  DL+A +  A+  ++  ++    + LDG
Sbjct: 556 PVVKNRIRSLDLAAAETLARTVMEQTDSGKIGQLLDG 592


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: 1265
Number of extensions: 82
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: 596
Length adjustment: 39
Effective length of query: 807
Effective length of database: 557
Effective search space:   449499
Effective search space used:   449499
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: 55 (25.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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