GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF in Pseudomonas putida KT2440

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_1109
         (481 letters)



>lcl|FitnessBrowser__Putida:PP_2694 PP_2694 Aldehyde dehydrogenase
           family protein
          Length = 480

 Score =  571 bits (1472), Expect = e-167
 Identities = 275/475 (57%), Positives = 354/475 (74%)

Query: 5   KRYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGI 64
           K Y+NYI+G+W  G     N +PS+  D IG Y +A   Q   AI AARAA P W+ SG+
Sbjct: 4   KTYNNYIDGQWCEGHATLGNYSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGL 63

Query: 65  QARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGD 124
           ++R   L  +G E++AR+EELG LL+REEGK L E IGEV R+G  F ++A E LR  G+
Sbjct: 64  ESRQQVLMAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGE 123

Query: 125 YLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCA 184
              SVRPGV++EV RE +GVVG+ITPWNFP+A  AWKIAPALA+GN VV KPA+LVP  A
Sbjct: 124 TAASVRPGVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASA 183

Query: 185 WALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQ 244
           WAL EIISR G P+G FNLVMGSG  VG+AL+QS ++D ++FTGS+  GR++AV+     
Sbjct: 184 WALTEIISRQGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATAGNL 243

Query: 245 AKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAM 304
            + QLEMG KN  +++DDADL+ AVE ++  AF+ TGQ+CTASSR IV  GIHD+FVEA+
Sbjct: 244 VRCQLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHDRFVEAL 303

Query: 305 AERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYF 364
             RM+ +KVGHAL+ G  IGPV    QLEQ+L Y+ + Q+EGA L+ GG  +    +GY+
Sbjct: 304 RLRMRQLKVGHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQLACDGYY 363

Query: 365 LAPTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYAN 424
           + P LF +S   MRI+REE+FGP+A ++RV D+E ALA  NDTE+GL+AGI T SL++A+
Sbjct: 364 MRPALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIITQSLRHAS 423

Query: 425 HFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479
           HFKR +Q G VMVNLPTAG DYHVPFGGRK SS+G REQG+YA++FYTVVKT+Y+
Sbjct: 424 HFKRRAQTGCVMVNLPTAGTDYHVPFGGRKASSFGPREQGQYARDFYTVVKTTYL 478


Lambda     K      H
   0.318    0.134    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: 653
Number of extensions: 18
Number of successful extensions: 1
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: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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