GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Desulfotomaculum hydrothermale Lam5

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_008409656.1 DESHY_RS00685 ABC transporter ATP-binding protein

Query= TCDB::Q9X051
         (523 letters)



>NCBI__GCF_000315365.1:WP_008409656.1
          Length = 509

 Score =  307 bits (787), Expect = 5e-88
 Identities = 171/496 (34%), Positives = 290/496 (58%), Gaps = 5/496 (1%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQI 69
           + L+E + I+K FPGV+A + + LQ+ +GEV AL+GENG+GKSTLM IL+G+Y    G+I
Sbjct: 4   DFLVEMKQISKRFPGVLANDCIDLQVKRGEVLALLGENGSGKSTLMSILSGLYRPDAGEI 63

Query: 70  FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129
           ++EG++V F++PR+A + GI ++ Q    V   S AENI L  +   +  +++  K  ++
Sbjct: 64  YIEGRKVNFKSPRDAIDAGIGMVHQHFKQVDTFSVAENIILGSK--EKKCLLQAGKAEKE 121

Query: 130 ASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLF 189
            +++    G+ ++P  K+  LS +++Q V I K L   +K++I+DEPT+ +  +E  +LF
Sbjct: 122 IAEISRGYGLQVEPTAKIWQLSIAERQRVEIVKMLYRGSKVLILDEPTAVLTPQEARELF 181

Query: 190 NIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249
            +IR +   G+S+I I+H+L E+ E+ADRV ++R GR V     ++ +  +L RLM+G+ 
Sbjct: 182 QVIRQMTARGQSIILITHKLNEVMEVADRVTILRGGRAVATRERKQVNQRELARLMMGQD 241

Query: 250 IDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTEL 309
           +     K+     +EI R++     S D ++  + D++  VR+GE+LGI G+ G GR EL
Sbjct: 242 VVVPSQKQPGQFGEEILRLDRASAAS-DSRRPGLQDITLTVRQGEILGIAGIAGNGRREL 300

Query: 310 LEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITL 369
            E I G  P    GK++I GK++   SP + ++ G+  +PEDR   GL+  +  + N+ L
Sbjct: 301 AEVIAGLRP-LDGGKIYICGKDVTNLSPMEIIQEGVSYIPEDRLGTGLVPNLGAVDNLIL 359

Query: 370 PSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLA 429
                  + R    I  +   +     I ++ +K       V+ LSGGN Q+++LA+ LA
Sbjct: 360 KEYRRPWLSRG-PFICRRKAAQFATRLIHEVGVKVTGLDAPVKKLSGGNLQRLLLARELA 418

Query: 430 IKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEG 489
             PKV++   P RG+D+ A   ++K++ E    G  +V++S +L E+L +SD I V+ +G
Sbjct: 419 SSPKVIVAVYPVRGLDIAASEAVHKMLLEQRSKGAAIVLISEDLEELLKLSDNIGVLYKG 478

Query: 490 RKTAEFLREEVTEEDL 505
                   EE   E +
Sbjct: 479 SLMGVLPVEEAEPEKI 494



 Score =  103 bits (256), Expect = 2e-26
 Identities = 67/238 (28%), Positives = 125/238 (52%), Gaps = 11/238 (4%)

Query: 284 DDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKN 343
           D +   V++GEVL + G  G+G++ L+  + G +     G+++I G+++   SPRDA+  
Sbjct: 23  DCIDLQVKRGEVLALLGENGSGKSTLMSILSGLYRPDA-GEIYIEGRKVNFKSPRDAIDA 81

Query: 344 GIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIK 403
           GIG+V +  K        SV  NI L S   K +++       + EKEI    I +    
Sbjct: 82  GIGMVHQHFKQVDTF---SVAENIILGSKEKKCLLQA-----GKAEKEIAE--ISRGYGL 131

Query: 404 TPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSG 463
              P   +  LS   +Q+V + K L    KVL+LDEPT  +      E++++I +M   G
Sbjct: 132 QVEPTAKIWQLSIAERQRVEIVKMLYRGSKVLILDEPTAVLTPQEARELFQVIRQMTARG 191

Query: 464 MGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVETTQR 521
             +++++ +L E++ ++DR+ ++  GR  A   R++V + +L +  + + V V + ++
Sbjct: 192 QSIILITHKLNEVMEVADRVTILRGGRAVATRERKQVNQRELARLMMGQDVVVPSQKQ 249



 Score =  102 bits (255), Expect = 3e-26
 Identities = 63/227 (27%), Positives = 126/227 (55%), Gaps = 7/227 (3%)

Query: 28  VNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEVRFRNPREAQEN 87
           + ++TL + +GE+  + G  G G+  L +++AG+ P   G+I++ GK+V   +P E  + 
Sbjct: 274 LQDITLTVRQGEILGIAGIAGNGRRELAEVIAGLRPLDGGKIYICGKDVTNLSPMEIIQE 333

Query: 88  GIALIPQE---LDLVPNLSSAENIFLS--REPVNEFG-VIEYQKMFEQASKLFSKLGVNI 141
           G++ IP++     LVPNL + +N+ L   R P    G  I  +K  + A++L  ++GV +
Sbjct: 334 GVSYIPEDRLGTGLVPNLGAVDNLILKEYRRPWLSRGPFICRRKAAQFATRLIHEVGVKV 393

Query: 142 DP-KTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNIIRSLKNEGK 200
                 V+ LS    Q + +A+ L+   K+I+   P   +    +E +  ++   +++G 
Sbjct: 394 TGLDAPVKKLSGGNLQRLLLARELASSPKVIVAVYPVRGLDIAASEAVHKMLLEQRSKGA 453

Query: 201 SVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVG 247
           +++ IS  LEE+ +++D + V+  G  +G  P+EE + +K+  +M+G
Sbjct: 454 AIVLISEDLEELLKLSDNIGVLYKGSLMGVLPVEEAEPEKIGLMMLG 500


Lambda     K      H
   0.317    0.137    0.372 

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: 593
Number of extensions: 38
Number of successful extensions: 10
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: 523
Length of database: 509
Length adjustment: 35
Effective length of query: 488
Effective length of database: 474
Effective search space:   231312
Effective search space used:   231312
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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