GapMind for catabolism of small carbon sources

 

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

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000009985.1:WP_011383248.1
          Length = 485

 Score =  336 bits (862), Expect = 1e-96
 Identities = 196/474 (41%), Positives = 280/474 (59%), Gaps = 16/474 (3%)

Query: 24  INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83
           ING   ++ S  T   L+P +   + ++A+   A+  +AV  A+  F    W+ L PA +
Sbjct: 6   INGRQVESAS--TIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPK--WAGL-PASQ 60

Query: 84  KAKLIR-FADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           +AKL+R   DL+ ++V+E+A LE+LD G+    +  + +P AA   ++ A+    V  E 
Sbjct: 61  RAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGET 120

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
            PT +D L     +PVGVVG I PWN P + A WK  P LA GN+ VLK SE SPL+A R
Sbjct: 121 YPT-NDHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADR 179

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + QL +EAGIPAGV N++ GYG  VG+AL  H DV  + FTGST    +++   G   +K
Sbjct: 180 LGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGG---LK 236

Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322
           +  +E GGKSPNI+F D  D + A +AA  A+  N GE CT G+R+LV+  + D+F+  +
Sbjct: 237 KYSMELGGKSPNIIFDDC-DFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAAL 295

Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE----- 377
            E  +    G+PLD  T VG ++       V SYIE G  +GA+++AGG  T E      
Sbjct: 296 AERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHL 355

Query: 378 TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSD 437
             G +V PT+   V N+ R+AQEEIFGPV  VI F    EA+ IAN T YGLA+ +WT +
Sbjct: 356 KNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTEN 415

Query: 438 ISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            ++A + A  + AG V+VN  +  D+  PFGG K SG GR+   ++ E + E+K
Sbjct: 416 GARAIRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVK 469


Lambda     K      H
   0.316    0.132    0.390 

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: 630
Number of extensions: 28
Number of successful extensions: 5
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: 497
Length of database: 485
Length adjustment: 34
Effective length of query: 463
Effective length of database: 451
Effective search space:   208813
Effective search space used:   208813
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