GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_043743857.1
          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:

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