GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Desulfacinum hydrothermale DSM 13146

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_170920503.1 B9A12_RS09210 energy-coupling factor transporter ATPase

Query= uniprot:P70970
         (276 letters)



>NCBI__GCF_900176285.1:WP_170920503.1
          Length = 571

 Score =  142 bits (358), Expect = 2e-38
 Identities = 89/238 (37%), Positives = 132/238 (55%), Gaps = 11/238 (4%)

Query: 4   PFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKK 63
           P  R AL  I+ SI EG  +AV+GH GSGK+TL + L+GL  PT+G++      +   + 
Sbjct: 29  PNGRQALRHIDLSIHEGERIAVLGHNGSGKTTLARVLSGLAPPTQGRVLFQGDPLSRER- 87

Query: 64  NKDLKKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSE 123
              L+ LR++VG +FQ P+ QLF  TVL D+ FG +NF V  ++AE++AR+ L  +GL  
Sbjct: 88  ---LEDLRQRVGFLFQDPDDQLFCPTVLDDVLFGLLNFQVPPKEAEERARKALAAMGLEA 144

Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183
           E   R+P  LS GQ +R A+A +LA++P+VL+LDEPTA +DP     +  +  +      
Sbjct: 145 E-AHRAPHHLSYGQRKRAALAAILALEPDVLILDEPTANMDPTSEALLSKVLKDYPG--- 200

Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQ 241
            T I ++H +          +V+  G I    S   L      +   GLD   T +FQ
Sbjct: 201 -TLICISHDILFLYGLCTRAVVLQAGGIHHDTSFERLISHRASLQEHGLDF--TFRFQ 255



 Score =  116 bits (291), Expect = 1e-30
 Identities = 78/227 (34%), Positives = 123/227 (54%), Gaps = 12/227 (5%)

Query: 8   LALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDL 67
           +AL +++  +  G  +A++G  G+GKSTL   L G+   T   +  G  V  A ++N   
Sbjct: 326 VALENVSFQVGRGERLALVGPNGAGKSTLAACLAGIRWGTGQYLLDGRKVEGAFRRN--- 382

Query: 68  KKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLD 127
             L + VG+VFQ    Q+       +++FG  N G  +    +K + ML   GL E   D
Sbjct: 383 --LWRHVGLVFQDSADQMVCSRCGDEVAFGLRNLGWPESRIRKKVQAMLHWAGL-EGFED 439

Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187
           R P  LSGG+ +R+A+A VLAM+PEVL+LDEPTAGLDP+  ++++ +  E+      T +
Sbjct: 440 RVPQHLSGGERKRLALAAVLAMEPEVLILDEPTAGLDPQTEQKLLQLLDEV----EATLV 495

Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAG-WGLD 233
           L++H +   +   D  ++MH+G I     P   FL    +   +GLD
Sbjct: 496 LISHDVCFVSMLTDRTLLMHRGRI-VDDLPTGKFLVDRNLHSLYGLD 541


Lambda     K      H
   0.318    0.136    0.380 

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: 420
Number of extensions: 25
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 276
Length of database: 571
Length adjustment: 31
Effective length of query: 245
Effective length of database: 540
Effective search space:   132300
Effective search space used:   132300
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: 50 (23.9 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