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

GapMind for catabolism of small carbon sources

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

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_011383521.1 AMB_RS05630 amino acid decarboxylase

Query= BRENDA::A4Q8H0
         (720 letters)



>NCBI__GCF_000009985.1:WP_011383521.1
          Length = 783

 Score =  592 bits (1525), Expect = e-173
 Identities = 308/706 (43%), Positives = 431/706 (61%), Gaps = 32/706 (4%)

Query: 44  AKGMVTHLEEIGLNIPLFVAVCCE--EELDNAVLPALHGVFELCGKNTQFYGKQLEAAAV 101
           A  ++  +   GL +P+ + V  E  E++   VL  + G   L  +  +F  K L +   
Sbjct: 75  ATELINLMRRRGLEMPIVILVRGERFEDIPVDVLDYIDGYVFLAEETPEFIAKNLVSRLK 134

Query: 102 KYEKDLLPPFFNTLTQYVEMGNATFACPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCN 161
           ++ + L  PFF  L  Y E GN  + CPGH GG F+ + P GR F +  GE +FR D+ N
Sbjct: 135 QFAETLKTPFFGALVDYAEEGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAVFRDDLDN 194

Query: 162 ADVKLGDLLIHEGLPCAAQQHAAKVFNADKTYFVLNGTSASNKVATNALLTRGDLVLFDR 221
           + ++LGDLL HEG    AQ+ AAK+F A+KTYFVLNGTSASNK+  +AL+   DLVLFDR
Sbjct: 195 SVLELGDLLTHEGPALQAQKEAAKIFGAEKTYFVLNGTSASNKIVLSALVAEDDLVLFDR 254

Query: 222 NNHKSNHHGALIQAGATPVYLETARNPFGFIGGIDAHCFDERYLRQQIRE----VAPERA 277
           NNHK+ HHGAL+  G  P++LET RN  G IG I A  FDE+ +R +IR+      PE  
Sbjct: 255 NNHKAAHHGALLLGGGIPIFLETDRNAMGMIGPIYAEAFDEQAIRAKIRDNPLVKDPEAW 314

Query: 278 NEARPFRLAIIQLGTYDGTIYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLL 337
            + RPFR+A+I+  TYDGTIY+A  ++++IGHLCDYILFD AW G+ +F P+ + C  + 
Sbjct: 315 KKPRPFRVAVIEQCTYDGTIYSAEHILERIGHLCDYILFDEAWAGFLKFHPLFRGCYGMG 374

Query: 338 LE--LNENDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHAST 395
           L+  L+E+ PGII TQS HKQ AGFSQ SQIH +D+HIKGQSR   H+RFN  F+LHAST
Sbjct: 375 LKDRLDEDSPGIISTQSTHKQMAGFSQASQIHVRDRHIKGQSRRIEHRRFNETFLLHAST 434

Query: 396 SPFYPLFAALDVNAKMHEGKSGQRLWKECVRVGIEARKMLLETCQ-------------LI 442
           SPFYPLFA+LDV A+M  G+SG+ LW + + +GIE RK +    +               
Sbjct: 435 SPFYPLFASLDVGAQMMRGRSGEVLWDDTIDLGIELRKKVRAIKREFVEKEKDSARHWFF 494

Query: 443 KPFVPDQIDGK-------PWQSYDTETMANDLRFFNFVPGEKWHAFEGYAESQY-FVDPC 494
           +PFVPD++           W+   TET+A D R++ F PG +WH F+  + S Y   DP 
Sbjct: 495 EPFVPDRVPSPEGGETMVAWEDLPTETIAADPRYWEFTPGARWHGFKHVSRSGYAMTDPN 554

Query: 495 KLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSILFLLTPAEDIAKMQH 554
           KL L TPG +  +G Y+++GIPA ++A YLREN +VPEK DLNS+LFLLTP  + +K   
Sbjct: 555 KLTLITPGFNRDTGAYAEYGIPAPVVAQYLRENRVVPEKNDLNSMLFLLTPGVESSKAGT 614

Query: 555 LVALIARFEKHIEQDSLLSEVLPAVYKSNEQRYKNYTLRQLCQEMHDLYVSYDVKELQKE 614
           L++ +  F++  + ++LL + +P   +   QRY+   ++ LC EMH  +   +V  LQ+ 
Sbjct: 615 LLSSLVAFKRRHDDNALLDDAIPEFVRRRPQRYRGLRIQDLCAEMHAFFRDRNVSTLQRA 674

Query: 615 MFRKNYFPRIAMNPQDANTEFVRGNIELVSLAKAEGRIAAEGALPYPPGVLCVVPGEIWG 674
            F   + P + M P DA     R  ++ + + + +GRIA    + YPPG+  ++PGE   
Sbjct: 675 QFSPEHRPHMVMRPNDAVRMLTRNQVDYLPIDQIDGRIATTLWVVYPPGIATIIPGERLC 734

Query: 675 GAAQ---RYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYV 717
             A+    Y    E   NL PGF  E+QG+Y + + DG  R Y YV
Sbjct: 735 ERARPMLDYLKMFERSANLFPGFEAEIQGLYREIEPDGSIRFYTYV 780


Lambda     K      H
   0.321    0.138    0.420 

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: 1422
Number of extensions: 49
Number of successful extensions: 6
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: 720
Length of database: 783
Length adjustment: 40
Effective length of query: 680
Effective length of database: 743
Effective search space:   505240
Effective search space used:   505240
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 (21.9 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 paper from 2022 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