GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Marivita geojedonensis DPG-138

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_085640383.1 MGEO_RS16525 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::Phaeo:GFF1160
         (1158 letters)



>NCBI__GCF_002115805.1:WP_085640383.1
          Length = 1140

 Score = 1503 bits (3892), Expect = 0.0
 Identities = 788/1137 (69%), Positives = 890/1137 (78%), Gaps = 11/1137 (0%)

Query: 24   LRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAE 83
            LR  ID  TY D+A   D L A A L  TDR  I A A  LV +IR  S PGLMEVFL+E
Sbjct: 9    LRPLIDDNTYADEALKVDSLRATAQLTQTDRDAIKARATKLVTEIREDSRPGLMEVFLSE 68

Query: 84   YGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALM 143
            YGLST+EG+ALMCLAEALLRVPDA TIDALIEDKIAPS W  HLG+STS LVNASTWALM
Sbjct: 69   YGLSTEEGIALMCLAEALLRVPDAATIDALIEDKIAPSNWASHLGESTSPLVNASTWALM 128

Query: 144  LTGKVL-DEKRSPVSALRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGM 202
            LTGKVL DE+  PV  LRGA+KRLGEPVIRTAV RAMKEMG QFVLGETI+ AMKRAA M
Sbjct: 129  LTGKVLKDEQPGPVGHLRGAIKRLGEPVIRTAVGRAMKEMGAQFVLGETIQSAMKRAARM 188

Query: 203  EAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHP 262
            EAKGYTYSYDMLGEAARTE DA RYHL+YSRAISAIA A  S DIR NPGISVKLSALHP
Sbjct: 189  EAKGYTYSYDMLGEAARTETDARRYHLSYSRAISAIAEAAKSKDIRDNPGISVKLSALHP 248

Query: 263  RYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAG 322
            RYE AQ+ +V  ++VPRL+ LA LA++AG+GLN+DAEEADRLS+SL+VIE V+S+P+L G
Sbjct: 249  RYEEAQQDTVMNEVVPRLRTLAQLARSAGIGLNIDAEEADRLSVSLDVIETVLSEPSLKG 308

Query: 323  WDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPV 382
            WDGFGVVVQAYGPR G  +D LY++A R DR++MVRLVKGAYWDTE+KRAQV G+  FPV
Sbjct: 309  WDGFGVVVQAYGPRAGHVIDWLYNLAERLDRKIMVRLVKGAYWDTEIKRAQVAGLPAFPV 368

Query: 383  FTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGM 442
            FT K  TD+SYIANARKLL +TDRIYPQFATHNAHTV+AILHMA+D  +  +EFQRLHGM
Sbjct: 369  FTAKHHTDISYIANARKLLGMTDRIYPQFATHNAHTVAAILHMAED--RTLFEFQRLHGM 426

Query: 443  GETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVA 502
            GE LH++V +   T CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVD +VP   VA
Sbjct: 427  GEALHDIVKDDEGTRCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDTDVPAAEVA 486

Query: 503  ADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLL 562
            ADPF         L  GP+LF PERPNS G+DL H PT AAI+AAR P+    W A PL+
Sbjct: 487  ADPFDT--QAVPKLPTGPELFAPERPNSKGWDLTHRPTRAAIEAARKPFSGVQWTATPLV 544

Query: 563  AKAPETATTTDEPVRNPADL-TTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAA 621
            A   ET  T  +PV NPA    TVG V  A    + TA + ATPWNA A  RAEVLN+AA
Sbjct: 545  AGDAETGAT--DPVINPARPGDTVGSVTWATSGTVATACTVATPWNADAAERAEVLNKAA 602

Query: 622  DLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYYAARISAEPPVGVFTCISPWNF 681
            DLYEA+YGELFALL REAGK+L D VAELREAVDFLRYYAAR     P GVF CISPWNF
Sbjct: 603  DLYEAHYGELFALLAREAGKSLLDAVAELREAVDFLRYYAARAEGPDPQGVFACISPWNF 662

Query: 682  PLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAGAVGGA 741
            PLAIF+GQIAAAL  GNAVLAKPAEQTPLIA+RA+ LLHEAGVP +ALQLLPGAG VG A
Sbjct: 663  PLAIFTGQIAAALTTGNAVLAKPAEQTPLIAYRAVQLLHEAGVPTTALQLLPGAGDVGAA 722

Query: 742  LTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQS 801
            LTS+  V GVAFTGST TA  I  +MA+HL PGAPLIAETGGLNAMIVDSTALPEQAVQ+
Sbjct: 723  LTSNPAVKGVAFTGSTETAQIIHRSMAKHLAPGAPLIAETGGLNAMIVDSTALPEQAVQA 782

Query: 802  IIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETA 861
            I+ESAFQSAGQRCSALRCLY+QEDIA++ ++ML GAMDAL +GDPW   TD GP ID  A
Sbjct: 783  IVESAFQSAGQRCSALRCLYVQEDIAESFVEMLTGAMDALVIGDPWIYGTDVGPAIDAEA 842

Query: 862  RAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQ 921
            R GI++++DAA  EGRVL  +  P GGTFV PTLI ++GI  LE+EIFGPVLH+  FKS+
Sbjct: 843  RDGIISYVDAAEVEGRVLHRLPLPGGGTFVPPTLIRVSGIADLEREIFGPVLHIATFKSK 902

Query: 922  DLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEG 981
            D+D +I  IN T YGLTFGL TRIDDRVQ++ ++I AGN+YVNRNQIGAIVGSQPFGGEG
Sbjct: 903  DIDTVIDAINGTDYGLTFGLQTRIDDRVQHVSEQIKAGNIYVNRNQIGAIVGSQPFGGEG 962

Query: 982  LSGTGPKAGGPFYMMRFCAPDRQKSVDSWPS--DAPAMTMLPAPTGQPMQEITTSLPGPT 1039
            LSGTGPKAGGP Y+ RF       + D WPS      +T      G       T+LPGPT
Sbjct: 963  LSGTGPKAGGPNYLARFRRHPADTAGDVWPSQDSKDRLTKALTSAGGKASATKTTLPGPT 1022

Query: 1040 GESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTSGVI 1099
            GESN L+ +AR P+LCLGPGP+A  AQARAV ALGG A++A G +    L  +E + G I
Sbjct: 1023 GESNVLTAMARGPILCLGPGPEAAKAQARAVEALGGIAVKAEGGIAPDWLADLE-SEGAI 1081

Query: 1100 WWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALLGG 1156
            WWGD+ TAR + + LA R GPILPLI G+PDK     ERHVCVDTTA+GGNA LL G
Sbjct: 1082 WWGDDETARALRTELASRKGPILPLITGMPDKGHACHERHVCVDTTASGGNAQLLSG 1138


Lambda     K      H
   0.317    0.132    0.387 

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: 3260
Number of extensions: 147
Number of successful extensions: 7
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: 1158
Length of database: 1140
Length adjustment: 46
Effective length of query: 1112
Effective length of database: 1094
Effective search space:  1216528
Effective search space used:  1216528
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: 58 (26.9 bits)

This GapMind analysis is from Sep 24 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