GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Pseudomonas putida KT2440

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PP_2589 PP_2589 Aldehyde dehydrogenase family protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>FitnessBrowser__Putida:PP_2589
          Length = 497

 Score =  554 bits (1427), Expect = e-162
 Identities = 267/489 (54%), Positives = 352/489 (71%)

Query: 9   WEQRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARA 68
           W+QRA DL +   A I+G+  +A  G TF  ++P    +L ++A+C  A+   AV +AR 
Sbjct: 7   WQQRASDLYLPAHALIDGKPVNAQDGATFAAINPATNNVLAQVAACGHAEVDLAVASARR 66

Query: 69  TFSSGVWSRLAPSKRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQAL 128
            F  G W R+AP +RK  ++R A L+  H EELALL++L+MGKP+ D+ NIDVPG+A   
Sbjct: 67  AFEQGPWPRMAPGERKKVLLRLAELIMAHREELALLDSLNMGKPVMDAYNIDVPGSAHVF 126

Query: 129 SWSGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSV 188
           +W GEA+DKLYD+VA T  + L  +TRE +GVV A+VPWNFPL MA WKL PAL+ GNSV
Sbjct: 127 AWYGEALDKLYDQVAPTAANALATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSV 186

Query: 189 VLKPSEKSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKI 248
           VLKP+E+SP +ALR+A LA+EAG+P+GVLNV+PG G   G+AL LH DVD LVFTGST++
Sbjct: 187 VLKPAEQSPFSALRLAQLALEAGVPEGVLNVVPGLGEQAGQALGLHPDVDCLVFTGSTQV 246

Query: 249 AKQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRL 308
            K  M YS +SN+K++WLE GGKSPN+VF +  DL  AAE AA  I FNQGEVC+A SRL
Sbjct: 247 GKYFMQYSAQSNLKQVWLECGGKSPNLVFDNCQDLDLAAEKAAFGIFFNQGEVCSANSRL 306

Query: 309 LVERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLV 368
            V+R+I D F+  +    + W PGNPLDPA+  GA+VD  Q   + + I     +GA+LV
Sbjct: 307 YVQRAIHDEFIERLQAKARQWLPGNPLDPASRAGAIVDAGQTGRIEAAIVRAGQEGARLV 366

Query: 369 AGGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYG 428
            GG+R+  E    Y+EPTIF GV   M +A+EE+FGPVL+V AFDT E+A+ +AND+ YG
Sbjct: 367 CGGRRLTIEGSDNYIEPTIFAGVEGRMSLAREEVFGPVLAVSAFDTEEEAVRLANDSIYG 426

Query: 429 LAAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYT 488
           LAA+VW+ D ++ H  A+AL+AG+V VN  D  D+T PFGG KQSG GRD SLH+FDKY+
Sbjct: 427 LAASVWSDDFNQVHRVARALKAGTVSVNTVDALDVTVPFGGGKQSGFGRDLSLHSFDKYS 486

Query: 489 ELKSTWIKL 497
           +LK+TW +L
Sbjct: 487 QLKTTWYQL 495


Lambda     K      H
   0.316    0.132    0.389 

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: 711
Number of extensions: 30
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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 (21.6 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