Alignments for a candidate for prpE in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Dinoroseobacter shibae DFL-12

Align propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 3607411 Dshi_0825 AMP-dependent synthetase and ligase (RefSeq)

Query= metacyc::MONOMER-21334
         (629 letters)



>FitnessBrowser__Dino:3607411
          Length = 630

 Score = 1090 bits (2819), Expect = 0.0
 Identities = 516/627 (82%), Positives = 560/627 (89%)

Query: 1   MAYQDVYESWKSDPEAFWMEAAKSIDWVEAPSRALDDSNAPLYEWFTDAKVNTCWNAVDR 60
           M Y   Y +WK+DPE FWMEAA++IDWV  P  AL+  NAPLYEWFTDA+VNTC+NAVDR
Sbjct: 1   MTYSQTYAAWKNDPEGFWMEAAQAIDWVTPPGAALNSDNAPLYEWFTDAEVNTCFNAVDR 60

Query: 61  HVEAGRGEQTAIIYDSPITHTKRQISYVELRNRVAMLAGALRAKGVEKGDRVIIYMPMIP 120
           HV+AG G++ AII+DSP+THTK++I+Y EL+ RV++LAGALRAKG+EKGDRV+IYMPM+P
Sbjct: 61  HVQAGNGDRVAIIHDSPVTHTKQEITYAELQERVSLLAGALRAKGIEKGDRVLIYMPMVP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDAQPKAIIAASCGLEPGRVVHYKPLLD 180
           +ALEAMLACARLGA+HSVVFGGFAANELAVRIDDA PKAIIAASCG+EPGRVVHYKPLLD
Sbjct: 121 QALEAMLACARLGAIHSVVFGGFAANELAVRIDDATPKAIIAASCGIEPGRVVHYKPLLD 180

Query: 181 GAIDMAKHKPEFCVIFQREQEVAHLEEGRDYNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
           GAID+A HKP+FC+IFQREQEVAHLE GRD++WH  QYGV+PAECVPV GNHPAYILYTS
Sbjct: 181 GAIDLATHKPDFCLIFQREQEVAHLEPGRDFDWHEAQYGVDPAECVPVAGNHPAYILYTS 240

Query: 241 GTTGAPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTG PKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICY PLIHGN
Sbjct: 241 GTTGQPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYAPLIHGN 300

Query: 301 TTIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTAIRAVKREDPKGEMLAKYDLSHLKA 360
           TTIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTA+RAVKREDP GE + KYDLSHLK 
Sbjct: 301 TTIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTALRAVKREDPNGEFIGKYDLSHLKT 360

Query: 361 LYLAGERADPDTIIWAQKALSVPVIDHWWQTETGWTIAGNPLGIEELPTKLGSPAKAMPG 420
           +YLAGERADPDTI W    L VPVIDHWWQTETGW IA NP+GIE LP K+GSP+ AMPG
Sbjct: 361 VYLAGERADPDTIQWTMDKLGVPVIDHWWQTETGWAIAANPMGIEHLPVKIGSPSVAMPG 420

Query: 421 YDVQILDEGGHQMKPGELGAIAVKLPLPPGTLPGLWNAEARFRKSYLEHFPGYYETGDAG 480
           YDVQ+LDEGGH + PG LGAIAVKLPL PGTLP LW AE RF KSYL  FPGYYETGDAG
Sbjct: 421 YDVQVLDEGGHPVAPGTLGAIAVKLPLAPGTLPNLWQAEERFVKSYLTTFPGYYETGDAG 480

Query: 481 MIDEDGYLYIMARTDDVINVAGHRLSTGGMEEVLAGHEDVAECAVIGVSDDLKGQMPLGF 540
            IDEDGYLYIMARTDDVINVAGHRLSTG MEEVLA H DVAECAVIGVSD LKGQMPLGF
Sbjct: 481 YIDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGF 540

Query: 541 LCLNNGCNRDHGDVVKEVVKLVRDKIGPVAAFKLAVVVDRLPKTRSGKILRGTMVSIADG 600
           LCL+ G NR H ++ KE VKLVR+KIGPVAAFKLA VVDRLPKTRSGKILRGTMV+IADG
Sbjct: 541 LCLSAGVNRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600

Query: 601 KEYKMPATIDDPAILDEIKVALQSLGY 627
             +KMPATIDDPAILDEI  AL  LGY
Sbjct: 601 TPWKMPATIDDPAILDEITEALGKLGY 627


Lambda     K      H
   0.319    0.137    0.428 

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: 1629
Number of extensions: 55
Number of successful extensions: 1
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: 629
Length of database: 630
Length adjustment: 38
Effective length of query: 591
Effective length of database: 592
Effective search space:   349872
Effective search space used:   349872
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis