GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Azospirillum brasilense Sp245

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate AZOBR_RS29185 AZOBR_RS29185 aldehyde dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1109
         (481 letters)



>FitnessBrowser__azobra:AZOBR_RS29185
          Length = 478

 Score =  501 bits (1291), Expect = e-146
 Identities = 259/471 (54%), Positives = 327/471 (69%), Gaps = 4/471 (0%)

Query: 9   NYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARH 68
           N+I G  V G    AN NP+   + IG YA A + Q   A+ AA AA P W+ S  Q R 
Sbjct: 6   NWIAGRLVDGVRMEANRNPARPGEVIGHYAWASVEQAEEALGAAHAALPGWAASNPQTRS 65

Query: 69  DSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPS 128
           D L +VG E+ AR EELG LL REEGKTL E IGEV R+  IF + AGE LR  G+ LP 
Sbjct: 66  DVLRRVGDELNARAEELGALLTREEGKTLREGIGEVRRSAQIFHYAAGEPLRQGGEALPG 125

Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALA 188
           +R G    V+RE +GVV LITPWNFP+A+PAWK A ALA+GN VVLKP+++ P CAW LA
Sbjct: 126 LRDGTTAMVSREPVGVVVLITPWNFPMAVPAWKTAYALAFGNTVVLKPSEVTPACAWELA 185

Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248
           +I+ RAG PAG FNLV+G GR +G ALV     D +SFTGS GVGR I    V+R  +VQ
Sbjct: 186 DILHRAGLPAGAFNLVVGDGRTLGPALVDG--ADAVSFTGSPGVGRAILERSVARMTRVQ 243

Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERM 308
           LE+GGKNP ++ DDADL+ AV++++Q AF+STGQRCTA+SR IV   +HD FVE +  R+
Sbjct: 244 LELGGKNPLVVHDDADLELAVDIALQGAFHSTGQRCTATSRIIVDRRVHDAFVERLVTRI 303

Query: 309 KSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYFLAPT 368
            +++VG  +   TD+GPVVS+AQL +DL  I   +SEGA L  GGG +  D +GYFL PT
Sbjct: 304 AALRVGDPMDAATDMGPVVSEAQLAKDLHCIADARSEGAELAFGGGRM--DGDGYFLEPT 361

Query: 369 LFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKR 428
           LF  +  AMRI+R+E+FGPVA ++     + A+A+AND++  LS+GI T  L  A  F+R
Sbjct: 362 LFVGTDNAMRINRDEVFGPVACVIPADGLDHAIAIANDSDHALSSGIVTRGLASAETFRR 421

Query: 429 HSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479
            S+AG+VMVN PTAG+DYHVPFGGR  S YG REQG  A EF+T  KT+YI
Sbjct: 422 RSRAGLVMVNAPTAGIDYHVPFGGRGPSGYGGREQGSAAVEFFTEGKTAYI 472


Lambda     K      H
   0.318    0.134    0.391 

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: 604
Number of extensions: 19
Number of successful extensions: 3
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: 478
Length adjustment: 34
Effective length of query: 447
Effective length of database: 444
Effective search space:   198468
Effective search space used:   198468
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: 51 (24.3 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