Alignments for a candidate for odc in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Herbaspirillum seropedicae SmR1

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate HSERO_RS17280 HSERO_RS17280 lysine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__HerbieS:HSERO_RS17280
          Length = 750

 Score =  373 bits (958), Expect = e-107
 Identities = 227/674 (33%), Positives = 358/674 (53%), Gaps = 26/674 (3%)

Query: 63  KAIINKADETKFNIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLYDREIEAAAK 120
           +A +++      +IPI++   T  S  +  + + ++   I    +       R I   AK
Sbjct: 85  RAFVSEIRHKNADIPIYLYGETRTSRHIPNDVLRELHGFIHMFEDTPE-FVARHIIREAK 143

Query: 121 KYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICN 180
            Y DG+ PPFF+AL  Y + G+  + CPGH GG  F KSP G+ F+ F+GE + R+D+CN
Sbjct: 144 SYLDGLAPPFFRALVDYAQDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGERMLRADVCN 203

Query: 181 ADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDR 240
           A  +LG LL H GP  ++E++AAR+FNAD  YFV NGT+TSN +   + VAPGD+V+ DR
Sbjct: 204 AVEELGQLLDHTGPVANSERNAARIFNADHCYFVTNGTSTSNKMVWHSTVAPGDIVVVDR 263

Query: 241 NNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKI-AKVDPEKAKAK 299
           N HKS+ + +++  G  PV+L  +R+  G IG I  ++F  +SI++KI A     +AK K
Sbjct: 264 NCHKSILH-SIIMTGAIPVFLMPTRNHLGIIGPIPLEEFTLESIQKKIEANPFAREAKNK 322

Query: 300 RPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNL 359
           +P R+  I   TYDG +YN + + + +    + + FD AW+ +  F    KD    +  +
Sbjct: 323 KP-RILTITQSTYDGVVYNVETLKDMLDGEIETLHFDEAWLPHATFHDFYKD----MHAI 377

Query: 360 GPDDPG-----ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSST 414
           G D P      I  TQSTHK  AG SQASQI  ++S    +   ++   FN A++  +ST
Sbjct: 378 GKDRPRAKKSLIFSTQSTHKLLAGLSQASQILVRES----ETVKLDEDAFNEAFLMHTST 433

Query: 415 SPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKPW 474
           SP Y + A+ D+ A M E   G  L  ++++ +++ R+ + K            V G   
Sbjct: 434 SPQYSIIASCDVAAAMMEAPGGTALVEESILEALDFRRAMKKIDQEFGDEWWFQVWGPNS 493

Query: 475 QDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGI 534
             AD    + + + W  +    WHGF   A     +DP K  +  PG+ +  G++ + GI
Sbjct: 494 FAADG---IGEREDWVIKAEDDWHGFGNLAPGFNMLDPIKATIVNPGLAL-NGQFGETGI 549

Query: 535 PAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEV 594
           PA I+  YL EHG+I EK  L S   + T   T+ + + LVT + +F+     + P+  +
Sbjct: 550 PASIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNTLVTALQQFKDDYDKNQPIWRI 609

Query: 595 LPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVEL 654
           LP  +++   RYE   ++ LCQ++H+ Y+  +      EM+L    P  AM P  A  ++
Sbjct: 610 LPE-FAQRNPRYERLGLRDLCQQIHETYRAYDVARLTTEMYLSDMQP--AMKPSDAFSKM 666

Query: 655 LKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFLILEESINRFPGFA 714
                + VPL ++EG        PYPPGI  ++PGE + K    Y     +   +FPGF 
Sbjct: 667 AHREIERVPLDELEGRVTSILLTPYPPGIPLLIPGEIFNKTIVDYLKFARDFNEKFPGFE 726

Query: 715 PEIQGVYFEKENGK 728
            ++ G+   + NG+
Sbjct: 727 TDVHGLVKREVNGR 740


Lambda     K      H
   0.318    0.136    0.405 

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: 1257
Number of extensions: 62
Number of successful extensions: 8
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: 745
Length of database: 750
Length adjustment: 40
Effective length of query: 705
Effective length of database: 710
Effective search space:   500550
Effective search space used:   500550
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: 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