GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Pseudomonas fluorescens FW300-N1B4

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate Pf1N1B4_4229 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD

Query= reanno::Putida:PP_4493
         (1006 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4229
          Length = 944

 Score = 1650 bits (4274), Expect = 0.0
 Identities = 802/941 (85%), Positives = 869/941 (92%)

Query: 65   RVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAG 124
            R+ATLM E RF+Q+KLTPRGGGTGTNGQSLTDG+VVDLSRHMN +LEINV ERWVRVQAG
Sbjct: 2    RIATLMAESRFRQIKLTPRGGGTGTNGQSLTDGVVVDLSRHMNAVLEINVAERWVRVQAG 61

Query: 125  TVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLL 184
             VKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLL
Sbjct: 62   VVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLL 121

Query: 185  GGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLA 244
            GGERLHS P+ DA LE  CA  GR+GEVYR AR IQETQA+LIE+ FPKLNRCLTGYDLA
Sbjct: 122  GGERLHSQPLSDAELEVVCAQSGRIGEVYRTARLIQETQADLIESVFPKLNRCLTGYDLA 181

Query: 245  HLRDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALM 304
            HLRDE GRFNLNSVLCGAEGSLGY+VEAKLNVLPIPKY+VLVNVRY SFMDALRDANAL+
Sbjct: 182  HLRDEHGRFNLNSVLCGAEGSLGYIVEAKLNVLPIPKYSVLVNVRYASFMDALRDANALL 241

Query: 305  AHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQ 364
            AHKPLSIETVDSKVLMLAMKDIVWHSVAEYFP D ER TLGINLVEF G++  +V A+V 
Sbjct: 242  AHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPTDAERATLGINLVEFSGEDLTQVKARVA 301

Query: 365  AFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPP 424
            +F+ HLQ+DT++ERLGHTLAEG EAVTRVY MRKRSVGLLGNVEGE+RPQPFVEDTAVPP
Sbjct: 302  SFVAHLQADTTIERLGHTLAEGGEAVTRVYAMRKRSVGLLGNVEGEIRPQPFVEDTAVPP 361

Query: 425  EQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALT 484
            E+LADYIA FRALLD +GLAYGMFGHVDAGVLHVRPALDMKDP QAALVKPISDAVA LT
Sbjct: 362  EKLADYIAQFRALLDSHGLAYGMFGHVDAGVLHVRPALDMKDPAQAALVKPISDAVAELT 421

Query: 485  KRYGGLLWGEHGKGLRSEYVPEYFGELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLT 544
            +RYGGLLWGEHGKGLRSEYVP++FGELYPALQ LKGAFDPHNQLNPGKICTP  +A+GL 
Sbjct: 422  RRYGGLLWGEHGKGLRSEYVPDFFGELYPALQLLKGAFDPHNQLNPGKICTPPDAAQGLL 481

Query: 545  PVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKG 604
             V+ VTLRG+LDR IDERVWQ F +AVHCNGNGACYNYDP+DAMCPSWKATRERQHSPKG
Sbjct: 482  KVNEVTLRGELDRQIDERVWQSFGTAVHCNGNGACYNYDPDDAMCPSWKATRERQHSPKG 541

Query: 605  RASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAG 664
            RASL+REWLRLQG ANIDVL AAR K+SWL+GLP R+RNN AR++G+ DFSHEVYDAMAG
Sbjct: 542  RASLIREWLRLQGAANIDVLEAARGKLSWLRGLPTRMRNNLARSRGEADFSHEVYDAMAG 601

Query: 665  CLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNA 724
            CLACKSCAGQCP+KVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPY+A+APGLYNA
Sbjct: 602  CLACKSCAGQCPVKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYMAYAPGLYNA 661

Query: 725  VMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLV 784
            VMGS W+S+LLA  VGM+DSPLI+R++ QATLTRC+V +A+VPALRELT AQR+RS+VLV
Sbjct: 662  VMGSTWMSRLLARHVGMLDSPLINRYDLQATLTRCKVVVASVPALRELTIAQRQRSVVLV 721

Query: 785  QDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLK 844
            QDAFTRYFETPLL++FI LAH+LG+RVFLAPYSANGKPLHVQGFLGAFAKAAIRNA+QLK
Sbjct: 722  QDAFTRYFETPLLASFIQLAHQLGYRVFLAPYSANGKPLHVQGFLGAFAKAAIRNASQLK 781

Query: 845  ALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLMDVLPEQAPAAPGSFRL 904
            ALADC VPLVGLDPAMTLVYRQEYQKVPGL  CPKVLLPQEWL DVLPE    A  +FRL
Sbjct: 782  ALADCEVPLVGLDPAMTLVYRQEYQKVPGLNDCPKVLLPQEWLFDVLPENPHPATQTFRL 841

Query: 905  MAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQSW 964
            +AHCTEKTNVPAST QWE VFARLGLKLVTEATGCCGMSGTYGHEARNQ+TSRTIFEQSW
Sbjct: 842  LAHCTEKTNVPASTSQWEAVFARLGLKLVTEATGCCGMSGTYGHEARNQDTSRTIFEQSW 901

Query: 965  ATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVVLQYAQ 1005
            A KLDK GE LATGYSCRSQVKR   R++RHPLEVVL++A+
Sbjct: 902  AGKLDKTGEALATGYSCRSQVKRRANRQLRHPLEVVLEHAR 942


Lambda     K      H
   0.320    0.135    0.409 

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: 2696
Number of extensions: 88
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: 1006
Length of database: 944
Length adjustment: 44
Effective length of query: 962
Effective length of database: 900
Effective search space:   865800
Effective search space used:   865800
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: 57 (26.6 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