GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Azospirillum brasilense Sp245

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate AZOBR_RS18900 AZOBR_RS18900 peptidase

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



>FitnessBrowser__azobra:AZOBR_RS18900
          Length = 766

 Score =  322 bits (826), Expect = 5e-92
 Identities = 217/605 (35%), Positives = 323/605 (53%), Gaps = 28/605 (4%)

Query: 373 VEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIGPVLVRKPQVIDY 432
           V  L A GE   P   A     S  D A L A  +++G + + G+A+G  ++ +PQ+   
Sbjct: 168 VAELVAQGELVNPQEVA-----STGDPALLPA--RLSGTSLASGLAMGLAVIHRPQLTIR 220

Query: 433 PKRGESPVIELQRLDAALDKVHADIGTLIDESQVASI---RDIFTTHQAMLKDPALREEV 489
               E    EL RL+AA+  +H+ I  L++ + +A +   +DI  T++   +D      +
Sbjct: 221 QMVSEDAESELARLNAAIATMHSAIDDLLNAAALAGLSEPKDILETYRMFAEDRGWLSRI 280

Query: 490 QVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACLTGVEAEQ-- 547
           +  ++ GL+AE A  +       +   L D  + ER  DL D+  R+L  L G ++E   
Sbjct: 281 REAIRMGLTAEGAVQQVQNDTRARMSHLTDPYIRERLLDLEDLTNRLLQHLAGRKSEADG 340

Query: 548 -APDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIVGAGPGV 606
               E  +LV   + P+++   + +R+ G++   G  +SH  I+ARAL IP +V A   +
Sbjct: 341 GTLPEDIVLVARSMGPAELLDYDQRRLRGVILEEGSPSSHVCIVARALNIP-VVQAPDAL 399

Query: 607 LGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANER-RMDAAVTRDGHP 665
             +     +++DG+ G+  V P+   ++ A +E  A   RK    E  R   +VTRDG P
Sbjct: 400 NRIEPLDPVIVDGDHGQAFVRPA-EDIQMAFAEAVALRARKEQMYEAIRAQPSVTRDGVP 458

Query: 666 VEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEALEGRP 725
           + I  N G   + P   A GAEGIGL RTE+ FM  S  P+   Q   Y R+L+  + +P
Sbjct: 459 ISIQLNCGLLIDLPHLKASGAEGIGLYRTEIPFMVRSTYPDVHAQTDLYSRILDQTDDKP 518

Query: 726 LVVRTLDVGGDKPLPYWPMP-AEENPFLGVRGIRLSLQRPDILETQLRALLASADGRPLR 784
           +V RTLDVGGDK LPY      EENP LG R IR+ L  P +L  QLRALL ++ GRPL 
Sbjct: 519 VVFRTLDVGGDKMLPYIAASEGEENPALGWRAIRIGLDHPSLLRQQLRALLRASAGRPLS 578

Query: 785 IMFPMVGNIDEWRTAKAMVD----RLRVE--LPVADLQVGIMIEIPSAALIAPVLAQEVD 838
           +MFPM+  + E+  A+ ++D    RL+ +   P + ++VG MIE+P+     P L   VD
Sbjct: 579 VMFPMIAEVAEFDAARRLLDLEINRLKGQGGEPPSRVRVGTMIEVPALLWQLPALLPRVD 638

Query: 839 FFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAA 898
           F S+G+NDLTQY  A DRG+P  SG+ D L PA++ L+   VEA    G  V +CGE+A 
Sbjct: 639 FLSVGSNDLTQYIFASDRGNPRTSGRYDPLSPAMMSLLRRLVEACGDAGVPVSICGEMAG 698

Query: 899 DALAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAH----EVRA 954
             L    L+G+G   LS+S  S+  VK  +R LD A   R     L L G H    ++R+
Sbjct: 699 RPLDAMALIGIGFRTLSMSPPSVGPVKTMLRSLDVAVL-RQYMNGLYLRGDHSLRDKLRS 757

Query: 955 FVGEH 959
           F  +H
Sbjct: 758 FAKDH 762


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: 1578
Number of extensions: 76
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: 766
Length adjustment: 42
Effective length of query: 918
Effective length of database: 724
Effective search space:   664632
Effective search space used:   664632
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