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.
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:
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