GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Acidovorax sp. GW101-3H11

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1480
          Length = 486

 Score =  379 bits (972), Expect = e-109
 Identities = 200/462 (43%), Positives = 273/462 (59%)

Query: 13  IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72
           IDG+WVDA +G T+ V NPA G  IG + +AG A    A+AAA   F  W+   A +RA 
Sbjct: 18  IDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDRTAEDRAR 77

Query: 73  TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132
            +R+   L+ +  + +A +MT EQGKPL EAR E+  AA  IEWFA+E RR+YG ++P  
Sbjct: 78  ILRRWFELMLQHQEDLALIMTSEQGKPLAEARGEIAYAASYIEWFAEEARRIYGEVIPSP 137

Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192
            L  +  V +EPVG  AA TPWNFP   + RK++ ALA GC+ +VK   +TP S  A+  
Sbjct: 138 WLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQTPLSALAMAE 197

Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252
               AGVPAGV  ++ GD   I + L   PV+RK+TFTGST +G+ LA+     +K+ ++
Sbjct: 198 LAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQCAPTLKKMSL 257

Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312
           ELGG+AP IV EDAD+  AV  A  +K+RN GQ C+   R LV + + D F   L +   
Sbjct: 258 ELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDAFAEKLARTVA 317

Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372
            LKVG+GLEEG   G L +   LT + +++ +A+  GA + TGG R    G F+ PT++A
Sbjct: 318 ALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRRHALGGTFYEPTILA 377

Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432
           ++  D  +   E FGPVA +  F    EAI  AN   FGLA Y ++R    V  ++  L+
Sbjct: 378 DITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDVGRVWRVSGALQ 437

Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
            GM+ IN         PFGGVK SG G EG    +E Y+ TK
Sbjct: 438 YGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTK 479


Lambda     K      H
   0.318    0.134    0.393 

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: 661
Number of extensions: 31
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: 481
Length of database: 486
Length adjustment: 34
Effective length of query: 447
Effective length of database: 452
Effective search space:   202044
Effective search space used:   202044
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: 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