GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Verminephrobacter eiseniae EF01-2

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein

Query= reanno::BFirm:BPHYT_RS25810
         (796 letters)



>NCBI__GCF_000015565.1:WP_011810430.1
          Length = 798

 Score =  929 bits (2402), Expect = 0.0
 Identities = 487/799 (60%), Positives = 573/799 (71%), Gaps = 7/799 (0%)

Query: 2   SVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQL 61
           +VA+   +M+YGP  E   P  +WL  H   F HFI G + APA  E F    PAT E+L
Sbjct: 3   TVADILRTMDYGPCLEAAAPVHSWLDAHAHSFRHFIHGEFVAPAQNEYFEVFNPATEERL 62

Query: 62  AQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDNG 121
           A+VA G  ADID AVAAAR A P W  L G  RAR+LYA+AR +Q+H+R FAVLE +DNG
Sbjct: 63  ARVAHGSDADIDQAVAAARQALPAWSGLSGHQRARYLYAIARHLQKHARFFAVLETMDNG 122

Query: 122 KPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIAP 181
           K IRE+RDID+PLV RHF HHAGWAQL +SEF  +  +GV GQIVPWNFPLLMLAWK+AP
Sbjct: 123 KTIRESRDIDIPLVVRHFYHHAGWAQLLDSEFPAHQAVGVCGQIVPWNFPLLMLAWKVAP 182

Query: 182 AIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKIA 241
           A+A GN VVLKPAE+TPLTAL FAEL    GLPAGVLN+VTGDG TGA+LV H  VDKIA
Sbjct: 183 ALAAGNTVVLKPAEFTPLTALAFAELCVEVGLPAGVLNIVTGDGHTGASLVNHAGVDKIA 242

Query: 242 FTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVCC 301
           FTGST VGRLIR ATAG+ K L+LELGGKSPFIVFDDADLD AVEGVVD+IWFNQGQVCC
Sbjct: 243 FTGSTAVGRLIRRATAGTDKKLSLELGGKSPFIVFDDADLDAAVEGVVDSIWFNQGQVCC 302

Query: 302 AGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRRE 361
           AGSR+LVQE + ARF  KL+ RM  LR+G  LDKS D+GAIVD VQL+RI+ +VE+GR +
Sbjct: 303 AGSRILVQESVAARFGDKLRARMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRAD 362

Query: 362 GCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALANN 421
           G S WQ+     PS G FF PT    V  A  LAQEEIFGPV+++M FRT DEA+ALAN+
Sbjct: 363 GLSCWQTA-LDAPSSGHFFAPTFFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANH 421

Query: 422 SRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREGI 481
           SRYGLAAS+WSE I   L VA +LA+GVVW+N  N+FDAA GFGGYRESG+GREGGREG+
Sbjct: 422 SRYGLAASLWSENIDVCLTVAAQLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGREGM 481

Query: 482 YEYLKPRAWLKLAERRAAQDV-VRDAAALDP--LSNVTSIDRTAKLFIGGKQARPDSGYS 538
           +EYL P+ WL     + AQD  V+ AA L P       SIDR+AK +IGGKQ RPDSGYS
Sbjct: 482 HEYLVPK-WLHAPGAQQAQDAPVQVAAHLAPTEAGAARSIDRSAKFYIGGKQVRPDSGYS 540

Query: 539 LPVLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADE 598
             V +  G  +G    GNRKDIRNAVE AR A  WSQAS H RAQVL+Y AENL  RA  
Sbjct: 541 FGVRSGSGALLGHAGFGNRKDIRNAVETARKAGNWSQASGHARAQVLYYFAENLGARAQT 600

Query: 599 FVRQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVI 658
           F+  L   +G +EAAA  + +  + R+F YAA ADK DG+VH+     V LAM+EP GV+
Sbjct: 601 FIAHLQAIDGISEAAASQQFEQVLARVFHYAAMADKHDGSVHSTLTAHVTLAMNEPFGVV 660

Query: 659 GIACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVT 718
           G+  P   PLL  +SLA P LA GNRVV++P   + L   D YQV +TSD+P GVLNIV 
Sbjct: 661 GVRSPAHTPLLAALSLALPLLATGNRVVLVPPPDASLMFADLYQVLDTSDMPAGVLNIVW 720

Query: 719 GERGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDR-ASEG 777
           G+   L   L  HDDVDA+W FG AA +  V+  S GNLK T+V   RQ DW  R   +G
Sbjct: 721 GDSDELAEVLALHDDVDALWYFGPAAGAARVQAASAGNLKSTWVQ-RRQLDWTSREQGQG 779

Query: 778 RPFLRQAVQVKNIWIPYGD 796
             F+R A QVKN+WIPYG+
Sbjct: 780 GEFMRHATQVKNVWIPYGE 798


Lambda     K      H
   0.319    0.135    0.408 

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: 1712
Number of extensions: 73
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: 796
Length of database: 798
Length adjustment: 41
Effective length of query: 755
Effective length of database: 757
Effective search space:   571535
Effective search space used:   571535
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: 55 (25.8 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