Alignments for a candidate for paaZ2 in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Azospirillum lipoferum B510

Align 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC 1.2.1.91) (characterized)
to candidate WP_012977792.1 AZL_RS28140 phenylacetic acid degradation protein PaaN

Query= reanno::BFirm:BPHYT_RS17340
         (566 letters)



>NCBI__GCF_000010725.1:WP_012977792.1
          Length = 596

 Score =  659 bits (1699), Expect = 0.0
 Identities = 337/552 (61%), Positives = 397/552 (71%), Gaps = 5/552 (0%)

Query: 5   LFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQLDQPS 64
           LF  HE  L+KA+ A  +R YWS F EMPSP+ YGETA ADGEAAF  H +  F LDQP 
Sbjct: 45  LFETHEAMLRKAVEASRSRAYWSAFPEMPSPRAYGETAAADGEAAFAGHRDKPFALDQPG 104

Query: 65  TGETVGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEILARVNR 124
               VG E SPFGF LG+ YP ++  AL+ AA AA   WR AGP    GVCLEIL R+N 
Sbjct: 105 VTGRVGGERSPFGFDLGITYPVSDAEALVTAARAAMPGWRKAGPNGRAGVCLEILKRLNA 164

Query: 125 ASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEKPQGKNP 184
            SFEI  +VMHTTGQAFMMAFQAGGPHAQDR LEAV Y W  +        WEKPQGKNP
Sbjct: 165 RSFEIANAVMHTTGQAFMMAFQAGGPHAQDRGLEAVAYGWKAMTDQAPAARWEKPQGKNP 224

Query: 185 PLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILPLALTVR 244
           PL M KR+ VV RG GLV+GC TFPTWNGYPGLFA L TGN VIVKP P AILPLA+TV+
Sbjct: 225 PLVMDKRFEVVGRGVGLVIGCATFPTWNGYPGLFASLVTGNAVIVKPGPTAILPLAITVK 284

Query: 245 IARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLERNAHQA 304
            AR+VL E G DPN+VTL      DG + +DLALRPE+ +ID+TGST  G WLERNA  A
Sbjct: 285 TAREVLAECGLDPNLVTLAI---GDG-IARDLALRPEVAVIDYTGSTGFGDWLERNARHA 340

Query: 305 QVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRTAEGTLS 364
           QVYTEKAGVN +VID  DD K   RN+AF+L+LYSGQMCT  Q I+VP+ GI+     + 
Sbjct: 341 QVYTEKAGVNSVVIDGTDDPKGMVRNLAFTLSLYSGQMCTTTQVIFVPKDGIQAGGEHMG 400

Query: 365 FDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTLEHPAFA 424
           FD+V  A+AG V + ++DP RAVE+LGAIQ++    RIDEAA LG V + S  + HP F 
Sbjct: 401 FDQVVSALAGGVDRFLSDPDRAVEVLGAIQSDATLARIDEAATLGTVALPSRAIAHPKFP 460

Query: 425 GARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGALTLSVY 484
            AR+RTPL+L +DAA +  ++  E FGPI+ ++ TD TA SL+ A  +    GALT  +Y
Sbjct: 461 EARIRTPLLLTMDAA-EEDKYGHELFGPIAIIVKTDGTADSLERAARLTRTKGALTAGLY 519

Query: 485 STDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADAAFVA 544
           STD  +++ A +  +  GVALS+NLTGGVFVNQSAAFSDFHGTGANPAANAAL D AFVA
Sbjct: 520 STDPQLIERATDLFVEAGVALSVNLTGGVFVNQSAAFSDFHGTGANPAANAALCDLAFVA 579

Query: 545 NRFRVVQSRVHV 556
           +RFRVVQSRV V
Sbjct: 580 SRFRVVQSRVPV 591


Lambda     K      H
   0.318    0.133    0.394 

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: 910
Number of extensions: 29
Number of successful extensions: 3
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: 566
Length of database: 596
Length adjustment: 36
Effective length of query: 530
Effective length of database: 560
Effective search space:   296800
Effective search space used:   296800
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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
the source code
instructions for running GapMind on your computer

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