GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Sinorhizobium meliloti 1021

Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate SMa0260 SMa0260 GabD3 succinate-semialdehyde dehdyrogenase

Query= SwissProt::Q8GAI8
         (450 letters)



>FitnessBrowser__Smeli:SMa0260
          Length = 487

 Score =  487 bits (1253), Expect = e-142
 Identities = 246/444 (55%), Positives = 320/444 (72%)

Query: 1   MLATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLE 60
           +LA +A A+ EDA  A++AA AA   W  T  R R+EILRR + L+T  +E+ A L+ LE
Sbjct: 42  LLAEVADASIEDAQRAVDAADAAAAGWRATPARQRSEILRRWYQLMTQHAEELATLIALE 101

Query: 61  MGKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWN 120
            GK LA+ARGEVAY AEF RW++EE  R  G +  TP G + ILV H+P+G  +LITPWN
Sbjct: 102 NGKALADARGEVAYAAEFFRWYAEEATRIPGEFRHTPSGSHNILVDHEPIGIAVLITPWN 161

Query: 121 FPLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGI 180
           FP AMATRK+ PA+AAGCT++LKPA  TPLT+   A+   EAG+P GV+NV+++S+  GI
Sbjct: 162 FPAAMATRKIGPALAAGCTVILKPASETPLTAYAMARLGEEAGVPPGVVNVLTTSNPGGI 221

Query: 181 SGPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEG 240
           +  +L D R+RK+SFTGST VG+ L+++A++ V+  SMELGGNAPF+VF+DADL+ A++G
Sbjct: 222 TNAMLADPRVRKLSFTGSTGVGRVLLAEAAKSVVSCSMELGGNAPFIVFDDADLEVALDG 281

Query: 241 AMAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGA 300
           AM AKMRN GEACTAANRF VQ  +   F     A M +L  G G DP +Q GP+I   A
Sbjct: 282 AMIAKMRNAGEACTAANRFYVQAGIHDAFVAGLTARMKSLKLGPGYDPETQCGPMITQNA 341

Query: 301 RDDIHALVTAAVDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTT 360
              I  LV+ A+ AGA A TGG P+   GYFY PTVL +VP NA+I  +EIFGPVAPV  
Sbjct: 342 VRKIDRLVSEALAAGARATTGGKPLTENGYFYPPTVLENVPVNASIAREEIFGPVAPVYK 401

Query: 361 FTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVK 420
           F ++ +AI+LAN +EYGLAAY+YSRD  R ++V ++IE GM+G N G++S+ AAPFGGVK
Sbjct: 402 FESDDEAIRLANNTEYGLAAYIYSRDLKRAMKVGKRIETGMLGINRGLMSDPAAPFGGVK 461

Query: 421 QSGLGREGGSEGIAEYTTTQYIGI 444
           QSGLGREGG  GI E+   +Y  +
Sbjct: 462 QSGLGREGGVTGILEFMEPKYFAV 485


Lambda     K      H
   0.317    0.131    0.376 

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: 528
Number of extensions: 15
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: 450
Length of database: 487
Length adjustment: 33
Effective length of query: 417
Effective length of database: 454
Effective search space:   189318
Effective search space used:   189318
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.

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