GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Rhizobium etli CFN 42

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011427294.1 RHE_RS21035 propionyl-CoA synthetase

Query= reanno::Phaeo:GFF1175
         (629 letters)



>NCBI__GCF_000092045.1:WP_011427294.1
          Length = 636

 Score =  810 bits (2093), Expect = 0.0
 Identities = 388/631 (61%), Positives = 475/631 (75%), Gaps = 10/631 (1%)

Query: 3   YSEVYEGWKANPEQFWMEAAEAISWDSAPTKALTDKGDGLY-EWFADARVNTCYNAVDRH 61
           Y + Y  WK++PE FW EAA  I W   P +  +   +G+Y  WF+ A  NTC+N +DRH
Sbjct: 5   YHQTYAAWKSDPEAFWREAAADIDWFKPPERVYSPD-EGIYGRWFSGAETNTCHNCLDRH 63

Query: 62  VEQGRGEQTAIIYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPE 121
           V  GRG +TAII+DS +T  KR  SY E+   V  +A  L A G+ +GDRVI+YMPM+P+
Sbjct: 64  VRAGRGGETAIIFDSAMTGEKRRFSYDEVLGEVKAIAETLLALGIARGDRVILYMPMLPQ 123

Query: 122 ALEAMLACARLGAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDG 181
           A+ +MLACAR+GAVHSVVFGGFAA+ELA RIDD+  + +I ASCGLEPGR V YKPL+D 
Sbjct: 124 AVFSMLACARIGAVHSVVFGGFAASELAARIDDSGARLVITASCGLEPGRVVAYKPLVDQ 183

Query: 182 AIDLATHKPDFCVIFQREQEVAELIEGRDVNWHGFQYGVEP-----AECVPVEGNHPAYI 236
           AI++A  KP+ C++ QR Q  AEL+ GRD +   F+  V P       CV V    P YI
Sbjct: 184 AIEIARMKPERCLVLQRPQLRAELVGGRDED---FEAAVAPHRGAEVACVSVRATDPLYI 240

Query: 237 LYTSGTTGQPKGVIRHTAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPL 296
           LYTSGTTGQPKGV+R   G +VALNW+M+NIY + PG+VFW ASD+GWVVGHSYI Y PL
Sbjct: 241 LYTSGTTGQPKGVVRDNGGHMVALNWSMRNIYGLKPGEVFWTASDIGWVVGHSYIVYAPL 300

Query: 297 IHGNTTIVFEGKPIGTPDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLS 356
           I G TT++FEGKP+GTPDAG FWR+++EH V+  FTAPTAFRA++RED  GE + +Y++ 
Sbjct: 301 ISGVTTLIFEGKPVGTPDAGAFWRIVAEHDVRVLFTAPTAFRAIRREDGDGELIARYNMP 360

Query: 357 CLKQVYLAGERADPDTITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAV 416
            L+ ++LAGERADP+T+ WA+  L +PVIDHWWQTETGW IAANPLG+  LP K GSPA 
Sbjct: 361 NLRALFLAGERADPETLKWAERMLAIPVIDHWWQTETGWPIAANPLGLGALPVKHGSPAQ 420

Query: 417 PMPGYTVDILDEGGHPVAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYET 476
           PMPGY V +LD+ GHPV  G LG I ++LPLPPG LPTLW+A+DRF+ +YL  FPGYY+T
Sbjct: 421 PMPGYEVTVLDDAGHPVEAGTLGNIVIRLPLPPGCLPTLWHADDRFRSAYLDEFPGYYKT 480

Query: 477 GDAGMKDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQA 536
            DAG  DEDGYL+IM+RTDD+IN AGHRLSTGAMEEV A HPDVAECAVIGV D+LKGQA
Sbjct: 481 ADAGYVDEDGYLFIMSRTDDIINCAGHRLSTGAMEEVCARHPDVAECAVIGVIDALKGQA 540

Query: 537 PVGFLCLNAGCDTPHEDVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVN 596
           P GFL L          + A+VV ++R++IGPVAAFK A  V+RLPKTRSGKILRGTM  
Sbjct: 541 PCGFLVLKRHVLRESTAIEAEVVAMIRDQIGPVAAFKTAITVNRLPKTRSGKILRGTMQK 600

Query: 597 IADGTDWKMPATIDDPAILDEITTALQGLGY 627
           IADG  WKMPATIDDPAIL+EI  AL+  G+
Sbjct: 601 IADGIPWKMPATIDDPAILEEIAEALRKRGF 631


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: 1358
Number of extensions: 55
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: 629
Length of database: 636
Length adjustment: 38
Effective length of query: 591
Effective length of database: 598
Effective search space:   353418
Effective search space used:   353418
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 Apr 09 2024. 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