GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Herbaspirillum seropedicae SmR1

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate HSERO_RS01925 HSERO_RS01925 acetyl-CoA carboxylase biotin carboxylase subunit

Query= reanno::pseudo5_N2C3_1:AO356_01595
         (649 letters)



>FitnessBrowser__HerbieS:HSERO_RS01925
          Length = 459

 Score =  398 bits (1022), Expect = e-115
 Identities = 211/429 (49%), Positives = 281/429 (65%), Gaps = 4/429 (0%)

Query: 9   LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +L+ANRGEIA R+ R  R +G+ TV VHS  DR+A++ + AD  V +G + +  SYL + 
Sbjct: 5   ILIANRGEIALRIQRACRELGIKTVVVHSEADREAKYVKLADESVCIGPAPSTLSYLNMP 64

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128
            +I+AA+ + AQAIHPGYGFLSENA FA  +E +G +F+GP A  I  MG K +AK  M 
Sbjct: 65  AIISAAEVTDAQAIHPGYGFLSENADFAERVEKSGFVFIGPRAENIRMMGDKVSAKQAMI 124

Query: 129 TAGVPLVPGYHGEAQDL-ETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187
            AGVP VPG  G   D  +     A +IGYPV++KA  GGGG+GM+VV   + L  A+  
Sbjct: 125 RAGVPCVPGSDGALPDNPKEIVQIARKIGYPVIIKAAGGGGGRGMRVVHTEAALINAVTM 184

Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247
            + EA ++FG+  + +EKYL  PRHVEIQ+ AD+H   ++L ERDCS+QRRHQKV+EEAP
Sbjct: 185 TKTEAGAAFGNPEVYMEKYLENPRHVEIQILADEHKQAIWLGERDCSMQRRHQKVIEEAP 244

Query: 248 APGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307
           APG+  ++   +GE    A + + Y GAGT EFL +   EF+F+EMNTR+QVEHPVTE I
Sbjct: 245 APGIPRKIIEKIGERCAEACRKMNYRGAGTFEFLYE-NEEFYFIEMNTRVQVEHPVTEMI 303

Query: 308 TGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAE 367
           TG+D+V  QIR+A GE L   Q  + L GHAIE R+ AEDP   F+P+ GR+  +     
Sbjct: 304 TGVDIVQEQIRIAAGEKLRYRQRDIELKGHAIECRINAEDPFK-FIPSPGRITAWHVPG- 361

Query: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFL 427
           GPG RVDS    G  + P YD M+GK+IA+G  REQA  R+   L E V+ G+ TNI   
Sbjct: 362 GPGIRVDSHAYSGYFVPPNYDSMVGKVIAYGATREQAIRRMQIALSEMVVEGISTNIPLH 421

Query: 428 RRIVAHPAF 436
           R ++    F
Sbjct: 422 RELMVDARF 430


Lambda     K      H
   0.319    0.134    0.390 

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: 713
Number of extensions: 31
Number of successful extensions: 4
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: 649
Length of database: 459
Length adjustment: 35
Effective length of query: 614
Effective length of database: 424
Effective search space:   260336
Effective search space used:   260336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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