GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Pseudomonas fluorescens FW300-N2E2

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate Pf6N2E2_1919 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1919
          Length = 490

 Score =  411 bits (1056), Expect = e-119
 Identities = 219/477 (45%), Positives = 299/477 (62%), Gaps = 4/477 (0%)

Query: 1   MANVTYTDTQLLIDGEWV-DAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGF 59
           +A+  +    L IDGEW+ D  S    +V++P+T   +  V  A  ADL R LAAA+ GF
Sbjct: 10  IADADHPRVGLFIDGEWIFDRPS--CFEVLDPSTEASLTSVPGATTADLKRVLAAAERGF 67

Query: 60  EAWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFAD 119
           + WR  P  ER   + +A A VR R++ IAQ++T+E GK + +AR EV  +A   +W   
Sbjct: 68  KIWRDTPPAERNIIISRAIAGVRSRSEEIAQIITRENGKLIADARAEVERSASFFDWDMA 127

Query: 120 EGRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKA 179
           +  R YG IVP      Q++++++P+GPVAAFTPWN P++   RK+S AL  GCS ++KA
Sbjct: 128 QALRAYGTIVPGE-AQMQKSILRQPIGPVAAFTPWNVPLSAPSRKISGALCAGCSIILKA 186

Query: 180 PEETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQL 239
           PEETP +  A+++ F  AG+P GV+ LV+G+PA +SS LI  PV R VT TGS  VGK L
Sbjct: 187 PEETPGAAVAMVQCFERAGLPKGVLNLVFGNPALVSSTLIESPVTRMVTLTGSVAVGKHL 246

Query: 240 ASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSI 299
           + LAG  MK   MELGGHAPVIV E  + A   K A  +K R   Q C +P RFLVH SI
Sbjct: 247 SQLAGAAMKPVLMELGGHAPVIVCEGVNAAEIGKMALKSKIRINAQWCAAPGRFLVHESI 306

Query: 300 RDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERI 359
            DEF  A V  A+ ++V +G++    +G + + RRL AM   +D+A   G  +  GG R+
Sbjct: 307 YDEFVAAFVATADQVRVADGMDTKADIGPVTSVRRLAAMQHFVDDALARGGKVAVGGHRV 366

Query: 360 GSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTR 419
           G  G +FAPT++ + PLD  +  +EPFGPVA    F  L+EAI  +N L  GLA +AFT 
Sbjct: 367 GERGYYFAPTLLVDTPLDCAIMTDEPFGPVAVAVRFSTLDEAIEISNSLSVGLAAFAFTN 426

Query: 420 SFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           S      L++ L+VG+L IN    P P+ PFGGVKDSG G EGGP +L+ Y+V+K+V
Sbjct: 427 SLEQAERLSRELDVGVLSINHFGAPDPDTPFGGVKDSGIGREGGPWSLDSYMVSKTV 483


Lambda     K      H
   0.318    0.134    0.393 

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: 597
Number of extensions: 31
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: 490
Length adjustment: 34
Effective length of query: 447
Effective length of database: 456
Effective search space:   203832
Effective search space used:   203832
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