GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS30285
          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.

Links

Downloads

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:

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