GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Phaeobacter inhibens BS107

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF1015 PGA1_c10320 methylcrotonoyl-CoA carboxylase beta chain

Query= reanno::Smeli:SM_b21122
         (535 letters)



>FitnessBrowser__Phaeo:GFF1015
          Length = 527

 Score =  845 bits (2183), Expect = 0.0
 Identities = 412/526 (78%), Positives = 460/526 (87%)

Query: 10  PSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRLATLIDPGTP 69
           PSSE FK NR A  +A+  I +A   A  GGGE +R RH SRGK+LPR R+A L+DPG+P
Sbjct: 2   PSSEGFKQNREAHLDALGQISEAAETARMGGGEKSRARHESRGKMLPRRRVANLLDPGSP 61

Query: 70  FLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPLTVKKHLRAQ 129
           FLE+GATAA+ MY+  APGAG++ GIGR+  +E M+VCND TVKGGTY+P+TVKKHLRAQ
Sbjct: 62  FLEIGATAAHAMYDGAAPGAGVVAGIGRVHGQEVMVVCNDATVKGGTYFPMTVKKHLRAQ 121

Query: 130 EIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQIAVVMGSCT 189
           EIA ENRLPC+YLVDSGGANLP QDEVFPDRDHFGRIFYNQA MSA GI QIAVVMGSCT
Sbjct: 122 EIAEENRLPCIYLVDSGGANLPQQDEVFPDRDHFGRIFYNQARMSAKGIAQIAVVMGSCT 181

Query: 190 AGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTRLSGVADHLA 249
           AGGAYVPAMSD  IIV++QGTIFLAGPPLV+AATGEVVSAEDLGG DVHTRLSGVAD+LA
Sbjct: 182 AGGAYVPAMSDVTIIVKEQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADYLA 241

Query: 250 RDDAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTPYEIREVIAR 309
            DDAHALALARRAV +LN  KP TV    PE P YDPEEI G+VP DL+TPY+IREVIAR
Sbjct: 242 EDDAHALALARRAVQSLNITKPLTVNWASPEEPAYDPEEILGVVPGDLRTPYDIREVIAR 301

Query: 310 LVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFVELCAQRRIP 369
           LVDGSRFDEFK RFG TLV GFAHV G PVGI+ANNGVLFSE+A KGAHFVELC+QR+IP
Sbjct: 302 LVDGSRFDEFKPRFGETLVTGFAHVKGCPVGIIANNGVLFSEAAQKGAHFVELCSQRKIP 361

Query: 370 LVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAGNYGMCGRAF 429
           LVFLQNITGFMVGRKYE EGIA+HGAK+VTAVAT  VPK+TMLVGGSFGAGNYGM GRA+
Sbjct: 362 LVFLQNITGFMVGRKYENEGIARHGAKMVTAVATTNVPKVTMLVGGSFGAGNYGMSGRAY 421

Query: 430 SPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQPVLDLFERQS 489
            PRFLW+WPNSRISVMGGEQAAGVL++V+ +A++R G  WS EEEA F+QP +D+FE QS
Sbjct: 422 QPRFLWSWPNSRISVMGGEQAAGVLATVKRDAIERQGGSWSTEEEASFKQPTIDMFEEQS 481

Query: 490 HPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535
           HPLYASARLWDDG+IDPRKSRDVLALSLSAALNAPIE+TRFG+FRM
Sbjct: 482 HPLYASARLWDDGIIDPRKSRDVLALSLSAALNAPIEDTRFGVFRM 527


Lambda     K      H
   0.320    0.136    0.404 

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: 908
Number of extensions: 33
Number of successful extensions: 1
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: 535
Length of database: 527
Length adjustment: 35
Effective length of query: 500
Effective length of database: 492
Effective search space:   246000
Effective search space used:   246000
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 (21.8 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