GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Phyllobacterium brassicacearum STM 196

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_106711077.1 CU102_RS10565 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_04460
         (838 letters)



>NCBI__GCF_003010955.1:WP_106711077.1
          Length = 746

 Score =  253 bits (645), Expect = 4e-71
 Identities = 153/507 (30%), Positives = 259/507 (51%), Gaps = 9/507 (1%)

Query: 313 QLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALLEDPALLEAAIQSIDQGSA 372
           ++  L+ +L  +R  I + LS        E  ++  A+     D   +    ++I  G  
Sbjct: 207 EIDRLESSLGSLRISIDDMLSRRDVAFEGEHREVLEAYRMFAHDTGWVRRLEEAIRNGLT 266

Query: 373 ATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLGQDWHY---DVPAGAIV 429
           A  A  +        +  L +P + ER +D  DL  R+LR L+G+D       +   A++
Sbjct: 267 AEAAVEKVQSDTRARMMHLTDPYMRERLSDFDDLANRLLRQLMGRDVKTMAGSLAKDAVI 326

Query: 430 AAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGLPCLVALSASLLQQPQGQSV 489
            A  +  ++LL   ++ + GL + +G ATSHV I+AR  G+P    +   +       +V
Sbjct: 327 IARSMGAAELLDYPRERLRGLVLEDGAATSHVVIVARAMGIPVAGQVKGVVSMAENNDAV 386

Query: 490 VLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHTPAHTRDGLRIEVAANVASS 549
           ++D D GR+ L P S      ++  R   +R+   +     P+ ++DG+ I +  N    
Sbjct: 387 IVDGDDGRVHLRPQSDVEAAYSEKVRFRAKRQALYRELRDKPSVSKDGISISLLMNAGLL 446

Query: 550 NEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQAVLDAMGDKSVIIRTIDVGG 609
            +     + GA G+GL RTE  F+   T P  ++Q + Y++VL+A GD+ V  RT+D+GG
Sbjct: 447 VDLPQLAEAGAAGIGLFRTELQFMVASTFPRAEQQERLYRSVLEAAGDRPVTFRTLDIGG 506

Query: 610 DKQLDYLPLPA-EANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLQRCRILLPMVTEVD 668
           DK L Y      E NP +G R +R+   RP LL  Q+RALL+ +  +  R++LPMVTEV 
Sbjct: 507 DKVLPYFRSNVKEENPAMGWRALRLTLDRPGLLRTQVRALLKAAGGRELRLMLPMVTEVA 566

Query: 669 ELLYIRQRLDALCAELA-----LTQRLELGVMIEVPAAALLAEQLAEHADFLSIGTNDLS 723
           E+    + ++     L+     L  R+++G M+EVP+     ++L    DF+S+G+NDL 
Sbjct: 567 EVRKASELINREVQHLSRFAYDLPTRVKIGAMVEVPSLLWQLDELMSVVDFVSVGSNDLF 626

Query: 724 QYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRWVGVCGALASDPLATPVLIG 783
           Q+ +A+DR ++ +  R D L    LR++ Q      ++   V +CG +A  PL+   L+G
Sbjct: 627 QFVMAVDRGNSMITNRFDNLSVPFLRVLRQISEAGERNHTDVTLCGEMAGKPLSAMALLG 686

Query: 784 LGISELSVSPPQVGEIKERVRQLDAAD 810
           LG   +S+SP  +G +K  +  LD  +
Sbjct: 687 LGFRSISMSPAAIGPVKAMLGTLDIGE 713


Lambda     K      H
   0.318    0.133    0.379 

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: 1115
Number of extensions: 46
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: 838
Length of database: 746
Length adjustment: 41
Effective length of query: 797
Effective length of database: 705
Effective search space:   561885
Effective search space used:   561885
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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