GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Magnetospirillum magneticum AMB-1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= curated2:Q1QTQ7
         (489 letters)



>NCBI__GCF_000009985.1:WP_011383257.1
          Length = 499

 Score =  203 bits (516), Expect = 1e-56
 Identities = 156/471 (33%), Positives = 226/471 (47%), Gaps = 20/471 (4%)

Query: 4   KQQLLIDGAWVDGD-AARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62
           K    +DG WV  D   RF   DP +G  + +     AT+   A+ AA  A+  W +R+ 
Sbjct: 24  KSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPWRQRTA 83

Query: 63  AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122
            +R AV+  + + +  H++ LA  ++ E GKPL EA  E+         S  ++    G+
Sbjct: 84  KDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEIS-----YGASFISWFAEEGK 138

Query: 123 RA------RDIGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQ 176
           RA          D R ++  +P GV+A   P+NFP  +      PAL AG  VV KP+E 
Sbjct: 139 RAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAED 198

Query: 177 TPMTADLTLQCWLEAGLPAGVINLV--QGAAEVGQALAGSADIDGLLFTGSAKVGGLLHR 234
           TP++A    +    AGLP G+ N+V  +  A VG  + G+A +  L FTGS +VG LL  
Sbjct: 199 TPLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMA 258

Query: 235 QFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAV 294
           Q    V K+ +LELGGN P +V D  D +AAV   L S + + GQ C C  R +V  G +
Sbjct: 259 QCAETVKKV-SLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAG-I 316

Query: 295 GDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRR 354
            +D    L    A + V    S        L +  A   + A   D V++G R L+  R 
Sbjct: 317 YEDFAVKLAEKAAAMAVGHALSGVVQ-QGPLINAAAVAKVAAHVADAVSKGARVLTGGRP 375

Query: 355 LQAGTSLLSPG-LIDVTGCDVP-DEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIG 412
              G     P  L DVT   +   EE FGP+  + R+    EAIALAN + +GL+     
Sbjct: 376 HALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYS 435

Query: 413 GERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463
            + A        +  G+V  N ++  ++  APFGGI +SG  R  + Y  D
Sbjct: 436 RDVARVFRVAEALECGMVGVN-ESLISNEVAPFGGIKESGLGREGSKYGLD 485


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: 615
Number of extensions: 31
Number of successful extensions: 7
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: 499
Length adjustment: 34
Effective length of query: 455
Effective length of database: 465
Effective search space:   211575
Effective search space used:   211575
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 (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