GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N2E3

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate AO353_05300 AO353_05300 aldehyde dehydrogenase

Query= curated2:Q2SXN9
         (487 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05300
          Length = 481

 Score =  223 bits (568), Expect = 1e-62
 Identities = 167/469 (35%), Positives = 227/469 (48%), Gaps = 19/469 (4%)

Query: 5   FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64
           FI G WV GA           ++ + E A A    V  A+ +AR AF AWS   + AR  
Sbjct: 10  FIGGQWVAGAEYSININPSELSDVIGEYAKADLAQVNAAIDAARAAFPAWSTSGIQARSD 69

Query: 65  IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124
            + +  + ++ R+E L T++ RE GK L EA  EV+                +G+    +
Sbjct: 70  ALDKVGSEILARREELGTLLAREEGKTLPEAIGEVSRAGNIFKFFAGECLRLSGDYLPSV 129

Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183
             GV V +     GVV +  P+NFP  +P   I PAL  GN VV KP+EL PG A A  E
Sbjct: 130 RPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPAELVPGCAWALAE 189

Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242
           I   AG PAGV NLV G  +  G A+ N  ++DG+ FTGS   G  +      R +  + 
Sbjct: 190 IISRAGFPAGVFNLVMGSGRVIGDAMVNSPKVDGISFTGSVGVGRQIAVNCVSR-QAKVQ 248

Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302
           LEMGG NP ++ +  D+  AV  ++QSAF S GQRCT + R++V  G   D+FV  +A+ 
Sbjct: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAG-IHDKFVEAMAER 307

Query: 303 ASKIT---ASVFDADPQPFMGAVISARAASRLVAAQ---ARLVGLGASPIIEMKQRDPAL 356
              I    A     D  P +      +    +   Q   ARLV  G     + +      
Sbjct: 308 MKSIKVGHALKSGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVTCDTE------ 361

Query: 357 GFVNAAIL--DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQ 414
           G+  A  L  D      +  EE FGP+A IVR  D D A+A ANDT FGLSAG+     +
Sbjct: 362 GYYLAPTLFADSEAAMRISREEIFGPVANIVRVADYDAALAMANDTEFGLSAGIATTSLK 421

Query: 415 AWHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462
             + F+R  +AG+V  N PT G     PFGG  G S   R    YA ++
Sbjct: 422 YANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEF 470


Lambda     K      H
   0.320    0.134    0.402 

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: 497
Number of extensions: 18
Number of successful extensions: 4
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: 487
Length of database: 481
Length adjustment: 34
Effective length of query: 453
Effective length of database: 447
Effective search space:   202491
Effective search space used:   202491
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: 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