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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_011383257.1 AMB_RS04160 NAD-dependent
           succinate-semialdehyde dehydrogenase
          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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources