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

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacF 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources