GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Desulfobacter vibrioformis DSM 8776

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase

Query= curated2:Q1QTQ7
         (489 letters)



>NCBI__GCF_000745975.1:WP_035241269.1
          Length = 485

 Score =  208 bits (530), Expect = 3e-58
 Identities = 153/480 (31%), Positives = 236/480 (49%), Gaps = 41/480 (8%)

Query: 5   QQLLIDGAWVDGDAAR-FAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFA 63
           Q   I   W++ D+ +  A T+P +GE L T     A +   A+ AA  + P W  ++ A
Sbjct: 12  QACFIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPAWRSKTAA 71

Query: 64  ERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGER 123
           +R A++ R+ + L  ++E LA  +  E GKPL E+R       G++A + + +     E 
Sbjct: 72  QRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESR-------GEIAYAASFFEWFAEEA 124

Query: 124 ARDIGD--------ARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSE 175
            R  GD         R V+  +P GV+A   P+NFP  +       AL AG  +V KP+ 
Sbjct: 125 KRIYGDIIPQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPAT 184

Query: 176 QTPMTADLTLQCWLEAGLPAGVINLVQGAAE-VGQALAGSADIDGLLFTGSAKVGGLLHR 234
            TP +A    +   EAG+P GV N+V G++  +G  L  +  +  L FTGS +VG  L +
Sbjct: 185 ATPFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQ 244

Query: 235 QFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAV 294
              G + ++ ++ELGGN P +V D  D +AAV   L   + + GQ C CA RL V  G V
Sbjct: 245 DCAGTMKRV-SMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAG-V 302

Query: 295 GDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRR 354
            D   + L  A+A L+V     E       L  ++A + +    +D + +G + L+  +R
Sbjct: 303 YDQFCEKLARAVATLKVGNGIEE-GVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR 361

Query: 355 LQAGTSLLSPG-LIDVT-GCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIG 412
              G +  SP  L DVT    V  EE FGP   + ++    E +  ANDT YGL+A    
Sbjct: 362 HALGGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFT 421

Query: 413 ---------GERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463
                    GE+ ++   L+ I +GI+        +++ APFGG+ +SGN R  + Y  D
Sbjct: 422 RDMARTWRVGEKLEYG--LIGINSGII--------SNAVAPFGGVKESGNGREGSKYGLD 471


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: 603
Number of extensions: 27
Number of successful extensions: 6
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: 485
Length adjustment: 34
Effective length of query: 455
Effective length of database: 451
Effective search space:   205205
Effective search space used:   205205
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 Apr 09 2024. 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 (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