GapMind for catabolism of small carbon sources

 

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= reanno::Phaeo:GFF1175
         (629 letters)



>FitnessBrowser__Dino:3607411
          Length = 630

 Score = 1088 bits (2813), Expect = 0.0
 Identities = 517/627 (82%), Positives = 560/627 (89%)

Query: 1   MSYSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDR 60
           M+YS+ Y  WK +PE FWMEAA+AI W + P  AL      LYEWF DA VNTC+NAVDR
Sbjct: 1   MTYSQTYAAWKNDPEGFWMEAAQAIDWVTPPGAALNSDNAPLYEWFTDAEVNTCFNAVDR 60

Query: 61  HVEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIP 120
           HV+ G G++ AII+DSP+THTK+EI+Y EL+ RV+ LAGALRAKG+EKGDRV+IYMPM+P
Sbjct: 61  HVQAGNGDRVAIIHDSPVTHTKQEITYAELQERVSLLAGALRAKGIEKGDRVLIYMPMVP 120

Query: 121 EALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLD 180
           +ALEAMLACARLGA+HSVVFGGFAANELAVRIDDATPKAIIAASCG+EPGR VHYKPLLD
Sbjct: 121 QALEAMLACARLGAIHSVVFGGFAANELAVRIDDATPKAIIAASCGIEPGRVVHYKPLLD 180

Query: 181 GAIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTS 240
           GAIDLATHKPDFC+IFQREQEVA L  GRD +WH  QYGV+PAECVPV GNHPAYILYTS
Sbjct: 181 GAIDLATHKPDFCLIFQREQEVAHLEPGRDFDWHEAQYGVDPAECVPVAGNHPAYILYTS 240

Query: 241 GTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGN 300
           GTTGQPKGV+R TAG LVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICY PLIHGN
Sbjct: 241 GTTGQPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYAPLIHGN 300

Query: 301 TTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQ 360
           TTIVFEGKP+GTPDAGTFWRVISEHKVKSFFTAPTA RAVKREDP GEF+ KYDLS LK 
Sbjct: 301 TTIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTALRAVKREDPNGEFIGKYDLSHLKT 360

Query: 361 VYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPG 420
           VYLAGERADPDTI W  ++L VPVIDHWWQTETGW+IAANP+GIE LP K+GSP+V MPG
Sbjct: 361 VYLAGERADPDTIQWTMDKLGVPVIDHWWQTETGWAIAANPMGIEHLPVKIGSPSVAMPG 420

Query: 421 YTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAG 480
           Y V +LDEGGHPVAPG LGAIAVKLPL PGTLP LW AE+RF KSYLTTFPGYYETGDAG
Sbjct: 421 YDVQVLDEGGHPVAPGTLGAIAVKLPLAPGTLPNLWQAEERFVKSYLTTFPGYYETGDAG 480

Query: 481 MKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGF 540
             DEDGYLYIMARTDDVINVAGHRLSTGAMEEVLA HPDVAECAVIGVSD+LKGQ P+GF
Sbjct: 481 YIDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGF 540

Query: 541 LCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600
           LCL+AG + PH+++  + VKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG
Sbjct: 541 LCLSAGVNRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600

Query: 601 TDWKMPATIDDPAILDEITTALQGLGY 627
           T WKMPATIDDPAILDEIT AL  LGY
Sbjct: 601 TPWKMPATIDDPAILDEITEALGKLGY 627


Lambda     K      H
   0.318    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: 1632
Number of extensions: 59
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 ( 7.3 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 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