GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Azospirillum brasilense Sp245

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__azobra:AZOBR_RS19635
          Length = 485

 Score =  681 bits (1756), Expect = 0.0
 Identities = 334/482 (69%), Positives = 399/482 (82%), Gaps = 1/482 (0%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           + L D  L R QAYV+G W DA +G+T  V NPATGE +  V  +GA ETR+AI AAD A
Sbjct: 1   LSLNDQSLLRTQAYVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAA 60

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
           LPAWRA TAKERA  LRRWF+L++  Q+DLA LMT+EQGKPLAEA+GE+AY ASF+EWF 
Sbjct: 61  LPAWRAKTAKERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARGEVAYGASFIEWFA 120

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EE KR+YGD IP    +KRI+V+K+PIGV AAITPWNFP+AMITRK GPALAAGCT+V+K
Sbjct: 121 EEGKRVYGDVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVK 180

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAG-EVGGELTSNPIVRKLTFTGSTEIGR 239
           PA  TP SALALAELAERAG+P GVF++VTGS    +GGELT++PIVRKL+FTGSTE+G+
Sbjct: 181 PAEDTPLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGK 240

Query: 240 QLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQD 299
            LM + A  +KKVSLELGGNAPFIVFDDADLD AV+GAL SKYRN+GQTCVCANRL VQ 
Sbjct: 241 ILMRQSADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQA 300

Query: 300 GVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGK 359
           GVYDAF  KL  AV ++ +GNG+EAGVT GP+I+ +AV KVEE + DA++KGAKV  GGK
Sbjct: 301 GVYDAFAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGK 360

Query: 360 PHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFY 419
            H LGGTFFEPTIL  V     V+++E FGP+AP+F+F+ EA+ I M+NDTEFGLA+YFY
Sbjct: 361 RHGLGGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFY 420

Query: 420 ARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 479
           +RD+ RV+RVAEQLEYGMVGIN G++S EVAPFGGIK SG+GREGSKYG+ED+LEIKYLC
Sbjct: 421 SRDIGRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLC 480

Query: 480 LG 481
           +G
Sbjct: 481 VG 482


Lambda     K      H
   0.317    0.135    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: 702
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: 483
Length of database: 485
Length adjustment: 34
Effective length of query: 449
Effective length of database: 451
Effective search space:   202499
Effective search space used:   202499
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