GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011386738.1
          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:

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