GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Brucella inopinata BO1

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_008507649.1 BIBO1_RS12560 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::psRCH2:GFF3291
         (960 letters)



>NCBI__GCF_000182725.1:WP_008507649.1
          Length = 756

 Score =  304 bits (778), Expect = 2e-86
 Identities = 201/564 (35%), Positives = 306/564 (54%), Gaps = 22/564 (3%)

Query: 408 VNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVA 467
           V G   + GI +G V++ +P+++      E    EL RLD AL  +   I  ++    VA
Sbjct: 183 VTGHGFNDGIGLGHVVLHEPRIVVTNLFNEDSQAELNRLDEALGSLRISIDDMLSRRDVA 242

Query: 468 ---SIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEA-LHDKLLA 523
                R++   ++    D      ++  +  GL+AEAA +E+++S  + +   L D  + 
Sbjct: 243 VEGEHREVLEAYRMFAHDRGWVRRLEEAVHNGLTAEAA-VEKVQSDTRARMVHLTDPYMR 301

Query: 524 ERAADLRDVGRRVLACLTGVEAEQAPD---EPYILVMDEVAPSDVATLNAQRVAGILTAG 580
           ER +D  D+  R+L  L G + +   +   +  I+V   +  +++     +R+ G++   
Sbjct: 302 ERLSDFDDLANRLLRQLMGRDVKTIAESLAKDAIIVARSMGAAELLDYPRERLRGVVLED 361

Query: 581 GGATSHSAIIARALGIPAIVGAGPGVLGLARNT-LLLLDGERGELLVAPSGAQLEQARSE 639
           G ATSH  I+ARA+GIP +VG   GV+ +A N   +++DG+ G + + P  A +E A +E
Sbjct: 362 GAATSHVVIVARAMGIP-VVGQAKGVVSMAENNDAIIVDGDEGIVHLRPQ-ADVESAYAE 419

Query: 640 RAA-REERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVF 698
           +   R  R+    E R   A+T+DG  + +  N G   + P+  A GA GIGL RTEL F
Sbjct: 420 KVRFRARRQAHYRELRDKPAITKDGVDIALLMNAGLLVDLPQLSASGAAGIGLFRTELQF 479

Query: 699 MNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPA-EENPFLGVRGI 757
           M  S  P    QE  YR V++A   +P+  RTLD+GGDK LPY+   A EENP LG R I
Sbjct: 480 MVASTFPRSEQQERLYRSVIDAAGDKPVTFRTLDIGGDKVLPYFRATAQEENPALGWRAI 539

Query: 758 RLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDR-------LRVEL 810
           RL+L RP +L TQLRALL +A GR L++M PMV  + E + A+ +++R           L
Sbjct: 540 RLTLDRPGLLRTQLRALLKAAGGRELKLMLPMVTEVSEVKAAREIIEREVRHLSRFAHSL 599

Query: 811 PVADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHP 870
           P+  L++G M+E+P+       L   VDF S+G+NDL Q+ +A DRG+  +S + D L P
Sbjct: 600 PLC-LKLGAMVEVPALLWQLDELMTAVDFVSVGSNDLFQFLMAADRGNSLISDRFDQLSP 658

Query: 871 AVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRE 930
           + LR +   V+A   H K V +CGE+A   L    L+GLG   +S+SA +I  VKA +  
Sbjct: 659 SFLRALRHIVKAGARHDKPVTLCGEMAGRPLTAMTLIGLGFRSISMSAAAIGPVKAMLGA 718

Query: 931 LDFAACQRLAQQALMLP-GAHEVR 953
           LD      L  + L  P  AH +R
Sbjct: 719 LDAGKLNALLLEELNKPNNAHSLR 742


Lambda     K      H
   0.317    0.134    0.384 

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: 1386
Number of extensions: 74
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: 960
Length of database: 756
Length adjustment: 42
Effective length of query: 918
Effective length of database: 714
Effective search space:   655452
Effective search space used:   655452
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 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