GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Methylocella silvestris BL2

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_012591930.1 MSIL_RS15015 ribosome-associated ATPase/putative transporter RbbA

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_000021745.1:WP_012591930.1
          Length = 943

 Score =  122 bits (305), Expect = 8e-32
 Identities = 129/504 (25%), Positives = 219/504 (43%), Gaps = 57/504 (11%)

Query: 14  VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73
           V E   V+ R+G+  AL+DV+I +  G    L+G +G GKS+L+S++ G R+  +G+V  
Sbjct: 8   VGELYGVSLRYGARVALDDVTISLPAGRMVGLIGPDGVGKSSLLSLIAGARRIQSGQVHV 67

Query: 74  SGAAAPSIADRDAWRERVACVYQ--HSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDA 131
            G        R     ++A + Q     +  DLSV EN+        G +       RD 
Sbjct: 68  LGGDLGDPRHRADVCPQIAYMPQGLGKNLYPDLSVRENI-----EFFGRLFGQSKDERDR 122

Query: 132 R--ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189
           R  ALL    +D   D  A  LS   RQ + +  AL +    +ILDEPT  +D    ++ 
Sbjct: 123 RIAALLTATGLDPFPDRPASKLSGGMRQKLGLCCALIHDPDLLILDEPTTGVDPLSRRQF 182

Query: 190 FRRISEL--QREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSA---------PVSALP 238
           +  IS +  +R G++ +  + +++E  +    V +  DA  I++A           S+  
Sbjct: 183 WSLISRMRAERRGMSVIVATAYMEEADQFHWLVAM--DAGRILAAGSPSDLKAKTNSSSL 240

Query: 239 REQLIEAMTGERGGLAVADAAARGALPADTAVALELKELTG-----ADYEGVSFTVKRGE 293
            E  I  +  ER     A          D    +  ++LT         + VSF++KRGE
Sbjct: 241 EESFIALLPEERRRGHKAFTIGPRPPGDDGEPVIVARDLTRRFGEFVAVDRVSFSIKRGE 300

Query: 294 VVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHE 353
           + G  G+   G+++  + + GL  A  G   + G  +   D+ A    G        + E
Sbjct: 301 IFGFLGSNGCGKSTTMKMLTGLLPASAGEAFLFGEAVDASDMKARFRVGYMSQSFSLYSE 360

Query: 354 GLV---------LTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEH 404
             V         L     E A   IA +  +FG+     ++   Q+  D           
Sbjct: 361 LTVRQNLDLHAHLFHIAREKARARIADLTARFGL-----EDFLDQRTAD----------- 404

Query: 405 VVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVV-DRVREEGKAVLV 463
               L  G +Q++ +A A+   P +L+L +PT+GVD  +++    ++ D  R EG  + +
Sbjct: 405 ----LPLGIRQRLSLAVAIVHEPEILILDEPTSGVDPLARDRFWDLLADLSRGEGVTIFI 460

Query: 464 VSGELDDLRTCDRVLVMFRGRVAA 487
            +  +++   CDR+ +M  GRV A
Sbjct: 461 STHFMNEAARCDRIALMDAGRVLA 484



 Score = 91.7 bits (226), Expect = 1e-22
 Identities = 78/262 (29%), Positives = 122/262 (46%), Gaps = 11/262 (4%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72
           PV+ A ++T+RFG   A++ VS  +  GE    +G NG GKST + +LTGL     GE  
Sbjct: 272 PVIVARDLTRRFGEFVAVDRVSFSIKRGEIFGFLGSNGCGKSTTMKMLTGLLPASAGEAF 331

Query: 73  FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132
             G A  + +D  A R RV  + Q  ++  +L+V +NL ++        I  +  R    
Sbjct: 332 LFGEAVDA-SDMKA-RFRVGYMSQSFSLYSELTVRQNLDLHAHLFH---IAREKARARIA 386

Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192
            L   + ++   D R  DL +  RQ + +A A+ +    +ILDEPT+ +D     R +  
Sbjct: 387 DLTARFGLEDFLDQRTADLPLGIRQRLSLAVAIVHEPEILILDEPTSGVDPLARDRFWDL 446

Query: 193 ISELQR-EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAP----VSALPREQLIEAMT 247
           +++L R EGVT +FIS H       C  + ++   R + +      V A  R  L +A  
Sbjct: 447 LADLSRGEGVT-IFISTHFMNEAARCDRIALMDAGRVLATGTPAELVKARQRTNLEDAFI 505

Query: 248 GERGGLAVADAAARGALPADTA 269
                   A+A   G  P   A
Sbjct: 506 DYLEEANAAEARRSGPRPETAA 527



 Score = 71.6 bits (174), Expect = 1e-16
 Identities = 66/229 (28%), Positives = 111/229 (48%), Gaps = 13/229 (5%)

Query: 283 EGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHG 342
           + V+ ++  G +VGL G    G++S+   IAG R  + G + V G  L      A +   
Sbjct: 25  DDVTISLPAGRMVGLIGPDGVGKSSLLSLIAGARRIQSGQVHVLGGDLGDPRHRADVCPQ 84

Query: 343 IGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGP 402
           I  +P+    + L    SV EN      R+ G+    +  +++     ++ A G+    P
Sbjct: 85  IAYMPQGLG-KNLYPDLSVRENIEF-FGRLFGQ----SKDERDRRIAALLTATGL-DPFP 137

Query: 403 EHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREE--GKA 460
           +   S LSGG +QK+ +  AL  +P++L+L +PT GVD  S+    S++ R+R E  G +
Sbjct: 138 DRPASKLSGGMRQKLGLCCALIHDPDLLILDEPTTGVDPLSRRQFWSLISRMRAERRGMS 197

Query: 461 VLVVSGELDDLRTCDRVLVMFRGRVAAEFPAGWQDHDLIASVEGVSLHE 509
           V+V +  +++      ++ M  GR+ A   AG    DL A     SL E
Sbjct: 198 VIVATAYMEEADQFHWLVAMDAGRILA---AG-SPSDLKAKTNSSSLEE 242


Lambda     K      H
   0.318    0.134    0.377 

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: 950
Number of extensions: 46
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 510
Length of database: 943
Length adjustment: 39
Effective length of query: 471
Effective length of database: 904
Effective search space:   425784
Effective search space used:   425784
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.

Links

Downloads

Related tools

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