GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Burkholderia phytofirmans PsJN

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase

Query= reanno::WCS417:GFF827
         (481 letters)



>FitnessBrowser__BFirm:BPHYT_RS28770
          Length = 480

 Score =  632 bits (1631), Expect = 0.0
 Identities = 312/474 (65%), Positives = 375/474 (79%), Gaps = 1/474 (0%)

Query: 6   RFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQ 65
           +F N++ G+WV G D+  N+NPS+ SDVIG +A+A   Q   AI +AR+AF  WS S  Q
Sbjct: 3   QFKNFVGGEWVDGNDFAPNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQ 62

Query: 66  ARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDY 125
            R D LD+ GS ILAR+ ELG LLAREEGKTL EA+GEV RAG IFKFFAGE LR+ G+ 
Sbjct: 63  QRFDLLDQAGSTILARKNELGKLLAREEGKTLAEAVGEVGRAGQIFKFFAGEALRVGGEI 122

Query: 126 VPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAW 185
           +PSVRPG+ VEVTRE +GV+GLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPG  W
Sbjct: 123 LPSVRPGLTVEVTREPVGVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGSVW 182

Query: 186 ALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQA 245
            L +II+ AG PAGV NLVMG G +VG++LV S  VD +SFTGSVG G+ IA  CV+   
Sbjct: 183 ELVKIIAEAGAPAGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAIAAKCVATGK 242

Query: 246 KVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMA 305
           K QLEMGGKNP ++LDDADL  AVE  +  AFYSTGQRCTASSRLIVT+GIHD+FV AM 
Sbjct: 243 KFQLEMGGKNPMVVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSGIHDRFVEAML 302

Query: 306 ERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYL 365
            RM+S+K+G+AL + T IGPVV   QL+QD +YI++ ++EG   V GG  VT  TEG++L
Sbjct: 303 ARMRSLKIGNALDASTQIGPVVDAKQLEQDERYIELARNEGGS-VFGGERVTSATEGFFL 361

Query: 366 APTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425
           AP L  ++  AM I+REE+FGPVA+V++VA+YE ALA+AND+ FGLSAGI T SL +A+H
Sbjct: 362 APALVTNTTPAMTINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMSLAHASH 421

Query: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479
           FKRH QAGMVM+N  TAGVDYHVPFGGRKGSS G REQG YA+EFYT+VKT+Y+
Sbjct: 422 FKRHVQAGMVMINTATAGVDYHVPFGGRKGSSLGPREQGTYAREFYTIVKTAYV 475


Lambda     K      H
   0.318    0.134    0.390 

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: 667
Number of extensions: 15
Number of successful extensions: 2
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: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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