GapMind for catabolism of small carbon sources

 

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

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_043743857.1 AMB_RS08150 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1146
         (953 letters)



>lcl|NCBI__GCF_000009985.1:WP_043743857.1 AMB_RS08150
           phosphoenolpyruvate--protein phosphotransferase
          Length = 757

 Score =  324 bits (830), Expect = 2e-92
 Identities = 200/579 (34%), Positives = 307/579 (53%), Gaps = 22/579 (3%)

Query: 371 EEVEPLPAVSQHREVIADVAEVL----LAPASGSLI-----QAIAAAPGIAIGPAHIQVQ 421
           EE+E L  V+     +    E++    L P  G+ +     + +    G+ +G A +   
Sbjct: 146 EEIETLETVAMVLAELLVSGELVNRAELVPVDGNALLPLRMEGVKLNGGVGVGVAVLHRP 205

Query: 422 QVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAK--AIREIFITHQEMLDDPEL 479
           ++    L  E    E ERLK+AL  ++  +E L  R + +    R++  T++   +D   
Sbjct: 206 RITIQRLVAEDTDAELERLKKALTGIKLALEELFSRPEMRDGEHRDVLETYRMFAEDKGW 265

Query: 480 TDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVET 539
            + +   +  G +AEAA   V +    +   + D  L ER  D  D+  R+L  L+G + 
Sbjct: 266 LNRISEAIHTGLTAEAAVQKVHDDTRARMSQITDPYLRERMHDFEDLANRLLQHLAGGDD 325

Query: 540 PAEP-----EQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALV 594
              P      +  IL+   +GP ++   DP R+ G++   G AT+H AIVARAL IP + 
Sbjct: 326 DQRPGAADLPEGAILIGRNLGPMELFDYDPKRLRGLVLEEGSATSHVAIVARALDIPVVG 385

Query: 595 GAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALT 654
                +  ++P  P++ DG  G++ +       +   +    R+LR    A  R  PA+T
Sbjct: 386 RVKDVLDKIEPLDPVICDGDNGQVFIRPPDDIRETYIDAISQRQLRQAVYARLRELPAVT 445

Query: 655 TDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDG 714
                + +  N G    +    + GA+GIGL RTEL FMA S  PD A Q + Y+++LD 
Sbjct: 446 RQDVRIGIHMNAGLLLDLQHLHDSGADGIGLYRTELPFMARSSLPDVAAQTLLYKKILDQ 505

Query: 715 LAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADN 774
             G+P+V RTLDVGGDK LPYW   +E+NP LG R IR+TL RP VM +QLRALLRAA  
Sbjct: 506 AEGKPVVFRTLDVGGDKVLPYWNPYEEDNPALGWRSIRITLDRPAVMRSQLRALLRAAQG 565

Query: 775 RPLRIMFPMVGSVDEWRQARDMTER-LRLEIPVAD-----LQLGIMIEVPSAALLAPVLA 828
           R L +MFPM+  V E+ QAR + ++ L  E  + +     L++G M+EVP+ AL    L 
Sbjct: 566 RELSVMFPMIAEVSEFVQARLILDKELERERAMGNPMPSRLKVGTMLEVPALALQLDALL 625

Query: 829 KEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCG 888
             VDF S+G+NDLTQ+  A+DRG+P ++ + D L PA+++ +         +G  + VCG
Sbjct: 626 PMVDFVSIGSNDLTQFLFAVDRGNPRIAERYDSLAPAMVRFMRYVAAKCAQYGVTLSVCG 685

Query: 889 ELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIRELSL 927
           E+A  PL    L+G+G+  LS+S  +I  VK  +R L +
Sbjct: 686 EMAGRPLEAMALIGVGIRHLSLSAPNIGPVKTMVRSLDI 724


Lambda     K      H
   0.318    0.135    0.381 

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: 1340
Number of extensions: 60
Number of successful extensions: 3
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: 953
Length of database: 757
Length adjustment: 42
Effective length of query: 911
Effective length of database: 715
Effective search space:   651365
Effective search space used:   651365
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: 56 (26.2 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