GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000009985.1:WP_011383257.1
          Length = 499

 Score =  288 bits (738), Expect = 2e-82
 Identities = 173/481 (35%), Positives = 266/481 (55%), Gaps = 15/481 (3%)

Query: 18  IENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSL 77
           I++  +++G +  A +   F+ +DP T   +A +    + +  RA+ AA   +    W  
Sbjct: 23  IKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN--PWRQ 80

Query: 78  SSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDK 137
            +   R AV+    DL+ AH + LA L + + GKP+  ++  +I   A  I W+AE   +
Sbjct: 81  RTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAM-GEISYGASFISWFAEEGKR 139

Query: 138 VYGE-VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKS 196
            YG+ + TT+S    +++++P+GV+AA+ PWNFP+ +   K  PALAAG  V++KP+E +
Sbjct: 140 AYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDT 199

Query: 197 PLSAIRLAGLAKEAGLPDGVLNVVTGFGHEA-GQALSRHNDIDAIAFTGSTRTGKQLLKD 255
           PLSA+ LA LA  AGLP G+ N+VT     A G  ++ +  +  ++FTGSTR GK L+  
Sbjct: 200 PLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQ 259

Query: 256 AGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIA 315
             ++ +K+V LE GG +  IVF DC DL  A +   A  + N GQ CI   R L++  I 
Sbjct: 260 CAET-VKKVSLELGGNAPFIVFDDC-DLDAAVAGALASKYRNSGQTCICTNRFLVQAGIY 317

Query: 316 DEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGL 375
           ++F   L ++A     GH L      G LI+ A    V + + +  SKG  +L G   G 
Sbjct: 318 EDFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTG---GR 374

Query: 376 AAAIG-----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVW 430
             A+G     PT+  DV P     REE FGPV  + RF +E +A+ LAN S++GL    +
Sbjct: 375 PHALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFY 434

Query: 431 TRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490
           +RD++R  R++  L+ G V VN     +   PFGG K+SG GR+ S + L+ F E K + 
Sbjct: 435 SRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYVC 494

Query: 491 I 491
           I
Sbjct: 495 I 495


Lambda     K      H
   0.317    0.133    0.389 

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: 573
Number of extensions: 28
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: 495
Length of database: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
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: 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