GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Pedobacter sp. GW460-11-11-14-LB5

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein

Query= TCDB::Q88NY5
         (256 letters)



>FitnessBrowser__Pedo557:CA265_RS10520
          Length = 568

 Score =  128 bits (321), Expect = 3e-34
 Identities = 92/261 (35%), Positives = 148/261 (56%), Gaps = 19/261 (7%)

Query: 13  MISIKNVNKWY----GDFQVLTD-------CSTEVKKGEVVVVCGPSGSGKSTLIKCVNA 61
           ++ IKN+  WY    G F   TD        + EV  GE + + G SG GK+TL + +  
Sbjct: 309 LLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILR 368

Query: 62  LEPFQKGDIVVDGTSIAD-PKTNLPKLRSRVGMVFQ--HFELFPHLTITEN-LTIAQRKV 117
           L     G+I+ +G +I    KT L KLR  + ++FQ  +  L P L+I ++ L   Q   
Sbjct: 369 LIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQDPYASLNPKLSIGQSILEPLQVHK 428

Query: 118 LGRSEAEATKKGLALLDRVGLSA-HAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPT 176
           L R+++E  +K L LLD+VGL   H  ++P + SGGQ+QRV IARALA+ P  ++ DE  
Sbjct: 429 LYRNDSERKQKVLELLDKVGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDESV 488

Query: 177 SALDPEMVSEVLDVMVQLAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEF 235
           SALD  + ++VL+++  L  E G+T + ++H++   + +++R++ M+KG I E+   E+ 
Sbjct: 489 SALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPEQI 548

Query: 236 FGDQSARDQRTQHLLSKILQH 256
           F   + +   TQ L+  I  H
Sbjct: 549 F--YAPKAAYTQKLIEAIPGH 567



 Score =  106 bits (265), Expect = 9e-28
 Identities = 74/223 (33%), Positives = 124/223 (55%), Gaps = 12/223 (5%)

Query: 26  FQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQK----GDIVVDGTSIADPK 81
           F+ +   S +VKKG V+ + G SGSGKS     +  L   +     G+I  +  S+ +  
Sbjct: 20  FKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISLLNLS 79

Query: 82  TN-LPKLR-SRVGMVFQHFELFPHLTITENLTIAQRKVLGRS--EAEATKKGLALLDRVG 137
           +N + ++R +++ M+FQ      +   T    +A+  +L R   +AEA K  +AL + V 
Sbjct: 80  SNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIALFNEVQ 139

Query: 138 LSAHAK---KHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMVQL 194
           L    K    +P Q+SGGQ+QRV IA AL+ DP +++ DEPT+ALD  +   +L ++++L
Sbjct: 140 LPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQLLLKL 199

Query: 195 AQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFF 236
            QE  M M+ ++H++G   ++A+ V  M KG I+E    +  F
Sbjct: 200 KQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIF 242


Lambda     K      H
   0.319    0.134    0.383 

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: 324
Number of extensions: 22
Number of successful extensions: 9
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: 256
Length of database: 568
Length adjustment: 30
Effective length of query: 226
Effective length of database: 538
Effective search space:   121588
Effective search space used:   121588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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