GapMind for catabolism of small carbon sources

 

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

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_000009985.1:WP_011383248.1
          Length = 485

 Score =  338 bits (868), Expect = 2e-97
 Identities = 193/475 (40%), Positives = 279/475 (58%), Gaps = 16/475 (3%)

Query: 15  INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74
           ING     ++  TI   NPA  EVI  +   G AE  +A+ AA +A P W  L A +R+ 
Sbjct: 6   INGR--QVESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRAK 63

Query: 75  KLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIA-YAASFIEWFAEEAKRIYGDTIPG 133
            LR+  +L+ ++ D++A+L + + G+     K  +   AA    +FA+    + G+T P 
Sbjct: 64  LLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPT 123

Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193
           +  D     + QP+GV   I+PWN P    T K  P LA G T VLK +  +P SA  L 
Sbjct: 124 N--DHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLG 181

Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253
           +L   AGIPAGV ++V G    VG  L  +  VR +SFTGST  G ++++  +  +KK S
Sbjct: 182 QLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQ--SGGLKKYS 239

Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313
           +ELGG +P I+FDD D ++AV+ AI++ Y NNG++C    RI VQDG+YD F   LA   
Sbjct: 240 MELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERT 299

Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG---------KLIEGN 364
            K+ +G+ L+E T  GP+I      KV  +IE  +S+GA+V++GG          L  GN
Sbjct: 300 RKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLKNGN 359

Query: 365 FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRV 424
           F  PT+L DV  +  VA+EE FGP+A + RFKDEAE + ++N T +GLASY +  + +R 
Sbjct: 360 FVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARA 419

Query: 425 FRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479
            R+AE +E G+V +N+  + +   PFGGIK SG GREG  Y  E +LE+K +C+S
Sbjct: 420 IRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVS 474


Lambda     K      H
   0.317    0.134    0.384 

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: 644
Number of extensions: 27
Number of successful extensions: 4
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: 480
Length of database: 485
Length adjustment: 34
Effective length of query: 446
Effective length of database: 451
Effective search space:   201146
Effective search space used:   201146
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 (21.6 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