GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Burkholderia phytofirmans PsJN

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase

Query= curated2:Q1QTQ7
         (489 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS30285 BPHYT_RS30285
           succinate-semialdehyde dehydrogenase
          Length = 490

 Score =  220 bits (561), Expect = 8e-62
 Identities = 166/477 (34%), Positives = 235/477 (49%), Gaps = 29/477 (6%)

Query: 4   KQQLLIDGAWVDG-DAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62
           + Q LIDGAW    D ARFA T+P +GET+     + A     A  AA +AFP W     
Sbjct: 12  RPQNLIDGAWTGAADGARFAVTNPATGETIVEVADSGAADARAATDAAARAFPAWRDTLP 71

Query: 63  AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122
            ER  ++ R+   +  + + LA  ++ E GKPL EAR       G+VA   +       E
Sbjct: 72  RERAEILRRWHALIVANTDDLAKLMSMEQGKPLAEAR-------GEVAYGASYVAWFADE 124

Query: 123 RARDIGD--------ARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPS 174
             R  GD         R      P GV+A   P+NFP  +    I PAL AG  VV KP+
Sbjct: 125 ATRIYGDLIPQQQRGKRMSAVKEPVGVIAAITPWNFPLAMIARKIAPALAAGCTVVAKPA 184

Query: 175 EQTPMTADLTLQCWLEAGLPAGVINLV-----QGAAEVGQALAGSADIDGLLFTGSAKVG 229
           E TP+TA        EAGLP GV+N++     QG A V   LA S  +  + FTGS  VG
Sbjct: 185 EDTPLTALALAVLAQEAGLPDGVLNMLSASREQGIAAVADWLADSR-VRKITFTGSTPVG 243

Query: 230 GLLHRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIV 289
             L R+  G + K L+LELGGN P +V D  D +AAV  ++ + F +GGQ C C  R+ V
Sbjct: 244 KHLARESAGTLKK-LSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYV 302

Query: 290 PHGAVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPL 349
             G V +   D L   +  L+V AP ++P      + +  A   +    +D V  G + L
Sbjct: 303 QAG-VYERFADLLAKRVGALKV-APATDPQAQIGPMINERAIQKIARHVEDAVKHGAKVL 360

Query: 350 SRMRRL-QAGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGL 406
              +RL + G +  +P ++     D  V  EE FGP+  + R+ +  EAI L+NDT +GL
Sbjct: 361 VGGKRLTELGPNYYAPTVLTDARDDMLVSCEETFGPVAPLFRFNEEAEAIRLSNDTPFGL 420

Query: 407 SAGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463
           +A     +    +    ++ AG++  N     +S  APFGG+ +SG  R  + Y  D
Sbjct: 421 AAYFYTQDVRRINRVAAQLEAGVIGINEGAV-SSEAAPFGGVKESGYGREGSKYGLD 476


Lambda     K      H
   0.319    0.135    0.409 

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: 650
Number of extensions: 45
Number of successful extensions: 5
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: 489
Length of database: 490
Length adjustment: 34
Effective length of query: 455
Effective length of database: 456
Effective search space:   207480
Effective search space used:   207480
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 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